SMS (spermine synthase) - Rat Genome Database

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Gene: SMS (spermine synthase) Homo sapiens
Analyze
Symbol: SMS
Name: spermine synthase
RGD ID: 1345734
HGNC Page HGNC
Description: Predicted to have spermine synthase activity. Predicted to be involved in spermine biosynthetic process. Localizes to extracellular exosome. Implicated in syndromic X-linked intellectual disability Snyder type.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: MRSR; Snyder-Robinson X-linked mental retardation syndrome; spermidine aminopropyltransferase; SPMSY; SpS; SRS
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: LOC100132039   LOC100419037   LOC642590   LOC646347   SMSP1  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX21,940,709 - 21,994,837 (+)EnsemblGRCh38hg38GRCh38
GRCh38X21,940,709 - 21,994,837 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X21,958,827 - 22,012,955 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X21,868,763 - 21,922,876 (+)NCBINCBI36hg18NCBI36
Build 34X21,718,498 - 21,772,611NCBI
CeleraX26,079,796 - 26,133,909 (+)NCBI
Cytogenetic MapXp22.11NCBI
HuRefX19,699,279 - 19,753,795 (+)NCBIHuRef
CHM1_1X21,989,118 - 22,043,385 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Abnormality of the Leydig cells  (IAGP)
Abnormality of the pinna  (IAGP)
Absent speech  (IAGP)
Anteverted nares  (IAGP)
Arachnodactyly  (IAGP)
Asymmetry of the ears  (IAGP)
Bifid uvula  (IAGP)
Brachycephaly  (IAGP)
Broad-based gait  (IAGP)
Bulbous nose  (IAGP)
Camptodactyly  (IAGP)
Cerebral edema  (IAGP)
Cleft palate  (IAGP)
Cryptorchidism  (IAGP)
Cupped ear  (IAGP)
Decreased muscle mass  (IAGP)
Dental crowding  (IAGP)
Difficulty standing  (IAGP)
Disproportionate tall stature  (IAGP)
Dysarthria  (IAGP)
Ectopic kidney  (IAGP)
EEG abnormality  (IAGP)
Everted lower lip vermilion  (IAGP)
Facial asymmetry  (IAGP)
Focal motor seizure  (IAGP)
Generalized hypotonia  (IAGP)
Generalized myoclonic seizure  (IAGP)
High myopia  (IAGP)
High palate  (IAGP)
High, narrow palate  (IAGP)
Hyperextensibility of the finger joints  (IAGP)
Hypertelorism  (IAGP)
Hypospadias  (IAGP)
Hypotonia  (IAGP)
Inability to walk  (IAGP)
Infantile muscular hypotonia  (IAGP)
Intellectual disability  (IAGP)
Intellectual disability, mild  (IAGP)
Intellectual disability, profound  (IAGP)
Kyphoscoliosis  (IAGP)
Long face  (IAGP)
Long fingers  (IAGP)
Long hallux  (IAGP)
Long palm  (IAGP)
Long toe  (IAGP)
Low-set ears  (IAGP)
Mandibular prognathia  (IAGP)
Megalencephaly  (IAGP)
Myoclonus  (IAGP)
Narrow face  (IAGP)
Narrow mouth  (IAGP)
Narrow palm  (IAGP)
Nasal speech  (IAGP)
Osteoporosis  (IAGP)
Patchy hypo- and hyperpigmentation  (IAGP)
Pectus carinatum  (IAGP)
Pectus excavatum  (IAGP)
Prominent nasal bridge  (IAGP)
Proptosis  (IAGP)
Recurrent fractures  (IAGP)
Schizophrenia  (IAGP)
Seizure  (IAGP)
Short philtrum  (IAGP)
Short stature  (IAGP)
Slender toe  (IAGP)
Small earlobe  (IAGP)
Smooth philtrum  (IAGP)
Sparse eyebrow  (IAGP)
Synophrys  (IAGP)
Talipes equinovarus  (IAGP)
Tall stature  (IAGP)
Testicular atrophy  (IAGP)
Thick lower lip vermilion  (IAGP)
Thickened helices  (IAGP)
Unilateral ptosis  (IAGP)
Unsteady gait  (IAGP)
Upslanted palpebral fissure  (IAGP)
Webbed neck  (IAGP)
Wide intermamillary distance  (IAGP)
X-linked recessive inheritance  (IAGP)
References

Additional References at PubMed
PMID:5823961   PMID:7546290   PMID:8826448   PMID:9299240   PMID:9847074   PMID:12477932   PMID:12665801   PMID:14508504   PMID:15489334   PMID:15592455   PMID:15772651   PMID:16169070  
PMID:18367445   PMID:18550699   PMID:19206178   PMID:19277733   PMID:19322201   PMID:20059804   PMID:21152090   PMID:21318891   PMID:21647366   PMID:21873635   PMID:21900206   PMID:22258329  
PMID:22863883   PMID:22939629   PMID:23376485   PMID:23408511   PMID:23455922   PMID:23468611   PMID:23533145   PMID:23696453   PMID:23805436   PMID:25921289   PMID:26344197   PMID:26496610  
PMID:26761001   PMID:28675297   PMID:29791485   PMID:29955894   PMID:30021884   PMID:30575818   PMID:30733278   PMID:32416067   PMID:32591507   PMID:32694731   PMID:32838743  


Genomics

Comparative Map Data
SMS
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX21,940,709 - 21,994,837 (+)EnsemblGRCh38hg38GRCh38
GRCh38X21,940,709 - 21,994,837 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X21,958,827 - 22,012,955 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X21,868,763 - 21,922,876 (+)NCBINCBI36hg18NCBI36
Build 34X21,718,498 - 21,772,611NCBI
CeleraX26,079,796 - 26,133,909 (+)NCBI
Cytogenetic MapXp22.11NCBI
HuRefX19,699,279 - 19,753,795 (+)NCBIHuRef
CHM1_1X21,989,118 - 22,043,385 (+)NCBICHM1_1
Sms
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X156,226,847 - 156,275,283 (-)NCBIGRCm39mm39
GRCm39 EnsemblX156,226,851 - 156,275,283 (-)Ensembl
GRCm38X157,443,851 - 157,492,287 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX157,443,855 - 157,492,287 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X153,881,886 - 153,929,978 (-)NCBIGRCm37mm9NCBIm37
MGSCv36X152,788,059 - 152,836,139 (-)NCBImm8
CeleraX140,696,273 - 140,722,448 (-)NCBICelera
Cytogenetic MapXF4NCBI
cM MapX72.48NCBI
Sms
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X37,516,949 - 37,572,657 (+)NCBI
Rnor_6.0 EnsemblX40,363,646 - 40,415,109 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X40,363,646 - 40,415,110 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X40,674,244 - 40,725,968 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X58,816,210 - 58,870,980 (+)NCBIRGSC3.4rn4RGSC3.4
CeleraX38,144,381 - 38,195,833 (+)NCBICelera
Cytogenetic MapXq21NCBI
Sms
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555092,276,878 - 2,329,620 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555092,277,501 - 2,328,612 (+)NCBIChiLan1.0ChiLan1.0
SMS
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X21,952,477 - 21,980,209 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0X14,571,432 - 14,625,601 (+)NCBIMhudiblu_PPA_v0panPan3
SMS
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X17,749,020 - 17,803,351 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX17,749,530 - 17,802,999 (+)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.0X17,724,469 - 17,762,827 (+)NCBI
UMICH_Zoey_3.1X17,741,907 - 17,796,615 (+)NCBI
UNSW_CanFamBas_1.0X17,763,366 - 17,818,317 (+)NCBI
UU_Cfam_GSD_1.0X17,823,900 - 17,878,940 (+)NCBI
Sms
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X10,755,764 - 10,814,207 (+)NCBI
SpeTri2.0NW_0049366242,345,573 - 2,402,157 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMS
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX18,118,468 - 18,169,396 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X18,118,332 - 18,169,396 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X19,300,734 - 19,353,814 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SMS
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X20,418,435 - 20,475,227 (+)NCBI
ChlSab1.1 EnsemblX20,418,494 - 20,476,276 (+)Ensembl
Vero_WHO_p1.0NW_02366605622,273,775 - 22,330,746 (+)NCBI
Sms
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248296,883,018 - 6,931,646 (+)NCBI

Position Markers
DXS7924  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37X21,964,720 - 21,964,819UniSTSGRCh37
Build 36X21,874,641 - 21,874,740RGDNCBI36
CeleraX26,085,675 - 26,085,774RGD
Cytogenetic MapXp22.1UniSTS
HuRefX19,705,493 - 19,705,592UniSTS
SMS_8632  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37671,317,471 - 71,318,315UniSTSGRCh37
GRCh371160,865,491 - 160,866,339UniSTSGRCh37
Build 361159,132,115 - 159,132,963RGDNCBI36
Celera1133,933,683 - 133,934,531RGD
Celera671,705,885 - 71,706,729UniSTS
HuRef668,515,624 - 68,516,468UniSTS
HuRef1132,221,806 - 132,222,654UniSTS
L47638  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37X22,012,363 - 22,012,538UniSTSGRCh37
Build 36X21,922,284 - 21,922,459RGDNCBI36
CeleraX26,133,317 - 26,133,492RGD
Cytogenetic MapXp22.1UniSTS
HuRefX19,753,203 - 19,753,378UniSTS
WI-17538  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37X21,990,048 - 21,990,148UniSTSGRCh37
Build 36X21,899,969 - 21,900,069RGDNCBI36
CeleraX26,111,001 - 26,111,101RGD
Cytogenetic MapXp22.1UniSTS
HuRefX19,730,872 - 19,730,972UniSTS
GeneMap99-GB4 RH MapX97.2UniSTS
Whitehead-RH MapX18.1UniSTS
NCBI RH MapX43.0UniSTS
DXS7528  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37X21,979,316 - 21,979,540UniSTSGRCh37
Build 36X21,889,237 - 21,889,461RGDNCBI36
CeleraX26,100,269 - 26,100,493RGD
Cytogenetic MapXp22.1UniSTS
HuRefX19,720,094 - 19,720,318UniSTS
Whitehead-RH MapX18.2UniSTS
Whitehead-YAC Contig MapX UniSTS
NCBI RH MapX43.0UniSTS
G19647  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic MapXp22.1UniSTS
A001U03  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic MapXp22.1UniSTS
GeneMap99-GB4 RH Map6306.13UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1027
Count of miRNA genes:699
Interacting mature miRNAs:796
Transcripts:ENST00000379404, ENST00000404933, ENST00000415881, ENST00000457085, ENST00000478094
Prediction methods:Microtar, Miranda, Pita, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High 2 3 2 2 4 1 1 1 3 7
Medium 2429 2598 1669 570 1663 412 4296 2046 3633 416 1445 1599 172 1204 2737 4
Low 8 392 54 52 287 51 56 150 99 2 11 7 3 1 51 1 2
Below cutoff 1 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_009228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001258423 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_004595 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_005274582 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011545568 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017029753 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017029754 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017029755 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_024452427 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AD001528 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK293455 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK313834 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC009898 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC085621 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471074 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U53331 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U72789 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U73023 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Z49099 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000379404   ⟹   ENSP00000368714
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 EnsemblX21,940,715 - 21,994,473 (+)Ensembl
RefSeq Acc Id: ENST00000404933   ⟹   ENSP00000385746
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 EnsemblX21,940,709 - 21,994,837 (+)Ensembl
RefSeq Acc Id: ENST00000457085   ⟹   ENSP00000407366
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 EnsemblX21,941,045 - 21,978,111 (+)Ensembl
RefSeq Acc Id: ENST00000478094
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 EnsemblX21,940,778 - 21,977,989 (+)Ensembl
RefSeq Acc Id: NM_001258423   ⟹   NP_001245352
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X21,940,709 - 21,994,837 (+)NCBI
GRCh37X21,958,691 - 22,025,798 (+)NCBI
HuRefX19,699,279 - 19,753,795 (+)NCBI
CHM1_1X21,989,118 - 22,043,385 (+)NCBI
Sequence:
RefSeq Acc Id: NM_004595   ⟹   NP_004586
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X21,940,709 - 21,994,837 (+)NCBI
GRCh37X21,958,691 - 22,025,798 (+)NCBI
Build 36X21,868,763 - 21,922,876 (+)NCBI Archive
HuRefX19,699,279 - 19,753,795 (+)NCBI
CHM1_1X21,989,118 - 22,043,385 (+)NCBI
Sequence:
RefSeq Acc Id: XM_005274582   ⟹   XP_005274639
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X21,959,623 - 21,994,837 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011545568   ⟹   XP_011543870
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X21,941,207 - 21,994,837 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017029753   ⟹   XP_016885242
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X21,940,730 - 21,993,391 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017029754   ⟹   XP_016885243
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X21,959,882 - 21,993,384 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017029755   ⟹   XP_016885244
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X21,941,169 - 21,993,384 (+)NCBI
Sequence:
RefSeq Acc Id: XM_024452427   ⟹   XP_024308195
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X21,966,983 - 21,994,837 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_004586   ⟸   NM_004595
- Peptide Label: isoform 1
- UniProtKB: P52788 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001245352   ⟸   NM_001258423
- Peptide Label: isoform 2
- UniProtKB: P52788 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_005274639   ⟸   XM_005274582
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_011543870   ⟸   XM_011545568
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_016885242   ⟸   XM_017029753
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_016885244   ⟸   XM_017029755
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_016885243   ⟸   XM_017029754
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_024308195   ⟸   XM_024452427
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSP00000407366   ⟸   ENST00000457085
RefSeq Acc Id: ENSP00000385746   ⟸   ENST00000404933
RefSeq Acc Id: ENSP00000368714   ⟸   ENST00000379404
Protein Domains
PABS

Promoters
RGD ID:6809281
Promoter ID:HG_KWN:66230
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000379404,   OTTHUMT00000056030,   OTTHUMT00000056032,   OTTHUMT00000056033,   UC004DAF.1
Position:
Human AssemblyChrPosition (strand)Source
Build 36X21,868,516 - 21,869,352 (+)MPROMDB
RGD ID:13604912
Promoter ID:EPDNEW_H28640
Type:initiation region
Name:SMS_2
Description:spermine synthase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H28641  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X21,940,596 - 21,940,656EPDNEW
RGD ID:13604914
Promoter ID:EPDNEW_H28641
Type:initiation region
Name:SMS_1
Description:spermine synthase
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H28640  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X21,940,741 - 21,940,801EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_004595.5(SMS):c.329+5G>A single nucleotide variant Syndromic X-linked intellectual disability Snyder type [RCV000012389] ChrX:21972576 [GRCh38]
ChrX:21990694 [GRCh37]
ChrX:Xp22.11
pathogenic
NM_004595.5(SMS):c.166G>A (p.Gly56Ser) single nucleotide variant Inborn genetic diseases [RCV000210586]|Syndromic X-linked intellectual disability Snyder type [RCV000012390]|not provided [RCV000414369] ChrX:21967312 [GRCh38]
ChrX:21985430 [GRCh37]
ChrX:Xp22.11
pathogenic|likely pathogenic
NM_004595.5(SMS):c.395T>G (p.Val132Gly) single nucleotide variant Syndromic X-linked intellectual disability Snyder type [RCV000012391] ChrX:21977126 [GRCh38]
ChrX:21995244 [GRCh37]
ChrX:Xp22.11
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:3092486-155699618)x2 copy number gain See cases [RCV000050889] ChrX:3092486..155699618 [GRCh38]
ChrX:3010527..154929279 [GRCh37]
ChrX:3020527..154582473 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:20140-155699618)x3 copy number gain See cases [RCV000050810] ChrX:20140..155699618 [GRCh38]
ChrX:70140..154929279 [GRCh37]
ChrX:10140..154582473 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:20140-155699618)x1 copy number loss See cases [RCV000050811] ChrX:20140..155699618 [GRCh38]
ChrX:70140..154929279 [GRCh37]
ChrX:10140..154582473 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:10679-156022206)x1 copy number loss See cases [RCV000050699] ChrX:10679..156022206 [GRCh38]
ChrX:60679..155251871 [GRCh37]
ChrX:679..154905065 [NCBI36]
ChrX:Xp22.33-q28
pathogenic|conflicting interpretations of pathogenicity|conflicting data from submitters
GRCh38/hg38 Xp22.33-q28(chrX:10679-156013167)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000050385]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000050385]|See cases [RCV000050385] ChrX:10679..156013167 [GRCh38]
ChrX:60679..155242832 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:10679-156013167)x1 copy number loss Global developmental delay [RCV000050386]|See cases [RCV000050386] ChrX:10679..156013167 [GRCh38]
ChrX:60679..155242832 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:10679-156022206)x3 copy number gain See cases [RCV000050697] ChrX:10679..156022206 [GRCh38]
ChrX:60679..155251871 [GRCh37]
ChrX:679..154905065 [NCBI36]
ChrX:Xp22.33-q28
pathogenic|conflicting interpretations of pathogenicity|conflicting data from submitters
GRCh38/hg38 Xp22.33-11.22(chrX:10679-52809182)x1 copy number loss See cases [RCV000051026] ChrX:10679..52809182 [GRCh38]
ChrX:60679..52838206 [GRCh37]
ChrX:679..52854931 [NCBI36]
ChrX:Xp22.33-11.22
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:26101-155999293)x3 copy number gain See cases [RCV000052322] ChrX:26101..155999293 [GRCh38]
ChrX:76101..155228958 [GRCh37]
ChrX:16101..154882152 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:2790845-155699618)x3 copy number gain See cases [RCV000052359] ChrX:2790845..155699618 [GRCh38]
ChrX:2708886..154929279 [GRCh37]
ChrX:2718886..154582473 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:237659-156022362)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052327]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052327]|See cases [RCV000052327] ChrX:237659..156022362 [GRCh38]
ChrX:154326..155252027 [GRCh37]
ChrX:94326..154905221 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:27245-155996431)x3 copy number gain See cases [RCV000052324] ChrX:27245..155996431 [GRCh38]
ChrX:77245..155226096 [GRCh37]
ChrX:17245..154879290 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-11.3(chrX:675360-46016699)x3 copy number gain See cases [RCV000052328] ChrX:675360..46016699 [GRCh38]
ChrX:636095..45876134 [GRCh37]
ChrX:556095..45761078 [NCBI36]
ChrX:Xp22.33-11.3
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:40704-156022362)x3 copy number gain See cases [RCV000052325] ChrX:40704..156022362 [GRCh38]
ChrX:90704..155252027 [GRCh37]
ChrX:30704..154905221 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:26102-155996431)x1 copy number loss Global developmental delay [RCV000052986]|Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052987]|Intellectual functioning disability [RCV000052988]|Global developmental delay [RCV000052989]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052987]|See cases [RCV000052986] ChrX:26102..155996431 [GRCh38]
ChrX:76102..155226096 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q22.1(chrX:675360-100368517)x1 copy number loss See cases [RCV000053005] ChrX:675360..100368517 [GRCh38]
ChrX:636095..99623515 [GRCh37]
ChrX:556095..99510171 [NCBI36]
ChrX:Xp22.33-q22.1
pathogenic
GRCh38/hg38 Xp22.33-11.23(chrX:10679-48344725)x1 copy number loss See cases [RCV000052981] ChrX:10679..48344725 [GRCh38]
ChrX:60679..48204160 [GRCh37]
ChrX:679..48089104 [NCBI36]
ChrX:Xp22.33-11.23
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:14245-155999293)x1 copy number loss Hypoplastic left heart [RCV000052982]|See cases [RCV000052982] ChrX:14245..155999293 [GRCh38]
ChrX:64245..155228958 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-11.21(chrX:2769041-58055036)x1 copy number loss See cases [RCV000053007] ChrX:2769041..58055036 [GRCh38]
ChrX:2687082..58081470 [GRCh37]
ChrX:2697082..58098195 [NCBI36]
ChrX:Xp22.33-11.21
pathogenic
GRCh38/hg38 Xp22.33-11.21(chrX:26102-57302794)x1 copy number loss See cases [RCV000052990] ChrX:26102..57302794 [GRCh38]
ChrX:76102..57329227 [GRCh37]
ChrX:16102..57345952 [NCBI36]
ChrX:Xp22.33-11.21
pathogenic
GRCh38/hg38 Xp22.33-22.11(chrX:253129-23023165)x1 copy number loss See cases [RCV000052993] ChrX:253129..23023165 [GRCh38]
ChrX:169796..23041282 [GRCh37]
ChrX:109796..22951203 [NCBI36]
ChrX:Xp22.33-22.11
pathogenic
GRCh38/hg38 Xp22.33-11.1(chrX:253129-58271563)x1 copy number loss See cases [RCV000052994] ChrX:253129..58271563 [GRCh38]
ChrX:169796..58297997 [GRCh37]
ChrX:109796..58314722 [NCBI36]
ChrX:Xp22.33-11.1
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:26102-155996431)x3 copy number gain Global developmental delay [RCV000052984]|Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052985]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052985]|See cases [RCV000052984] ChrX:26102..155996431 [GRCh38]
ChrX:76102..155226096 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-11.21(chrX:10679-55550898)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052971]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052971]|See cases [RCV000052971] ChrX:10679..55550898 [GRCh38]
ChrX:60679..55577331 [GRCh37]
ChrX:679..55594056 [NCBI36]
ChrX:Xp22.33-11.21
pathogenic
GRCh38/hg38 Xp22.33-11.22(chrX:10479-54179172)x3 copy number gain See cases [RCV000053817] ChrX:10479..54179172 [GRCh38]
ChrX:60479..53957191 [GRCh37]
ChrX:479..54222330 [NCBI36]
ChrX:Xp22.33-11.22
pathogenic
NM_004595.5(SMS):c.174T>A (p.Phe58Leu) single nucleotide variant Syndromic X-linked intellectual disability Snyder type [RCV000055902] ChrX:21971900 [GRCh38]
ChrX:21990018 [GRCh37]
ChrX:Xp22.11
pathogenic
NM_004595.5(SMS):c.200G>A (p.Gly67Glu) single nucleotide variant Syndromic X-linked intellectual disability Snyder type [RCV000055903] ChrX:21971926 [GRCh38]
ChrX:21990044 [GRCh37]
ChrX:Xp22.11
pathogenic
NM_004595.5(SMS):c.443A>G (p.Gln148Arg) single nucleotide variant Syndromic X-linked intellectual disability Snyder type [RCV000055905] ChrX:21977174 [GRCh38]
ChrX:21995292 [GRCh37]
ChrX:Xp22.11
pathogenic
NM_004595.5(SMS):c.449T>C (p.Ile150Thr) single nucleotide variant Snyder Robinson syndrome [RCV000055906] ChrX:21977180 [GRCh38]
ChrX:21995298 [GRCh37]
ChrX:Xp22.11
pathogenic
NM_004595.5(SMS):c.983A>C (p.Tyr328Ser) single nucleotide variant Snyder Robinson syndrome [RCV000055907] ChrX:21992634 [GRCh38]
ChrX:22010752 [GRCh37]
ChrX:Xp22.11
pathogenic
NM_004595.5(SMS):c.104T>A (p.Met35Lys) single nucleotide variant not provided [RCV000081159] ChrX:21967250 [GRCh38]
ChrX:21985368 [GRCh37]
ChrX:Xp22.11
uncertain significance
NM_004595.5(SMS):c.983A>G (p.Tyr328Cys) single nucleotide variant Syndromic X-linked intellectual disability Snyder type [RCV000074415] ChrX:21992634 [GRCh38]
ChrX:22010752 [GRCh37]
ChrX:Xp22.11
pathogenic
NM_004595.5(SMS):c.1026A>C (p.Ser342=) single nucleotide variant History of neurodevelopmental disorder [RCV000717145]|Syndromic X-linked intellectual disability Snyder type [RCV000601014]|not provided [RCV000889845]|not specified [RCV000173807] ChrX:21992677 [GRCh38]
ChrX:22010795 [GRCh37]
ChrX:Xp22.11
benign|likely benign|conflicting interpretations of pathogenicity
GRCh38/hg38 Xp22.33-q28(chrX:10679-156022826)x4 copy number gain See cases [RCV000133654] ChrX:10679..156022826 [GRCh38]
ChrX:60679..155252491 [GRCh37]
ChrX:679..154905685 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
NM_004595.5(SMS):c.569C>T (p.Thr190Ile) single nucleotide variant History of neurodevelopmental disorder [RCV000716750]|not provided [RCV000930025]|not specified [RCV000179446] ChrX:21978023 [GRCh38]
ChrX:21996141 [GRCh37]
ChrX:Xp22.11
benign|likely benign
GRCh37/hg19 Xp22.33-11.21(chrX:70297-58066465)x3 copy number gain See cases [RCV000239834] ChrX:70297..58066465 [GRCh37]
ChrX:Xp22.33-11.21
pathogenic
NM_004595.5(SMS):c.978G>A (p.Ser326=) single nucleotide variant History of neurodevelopmental disorder [RCV000718834]|not provided [RCV000173806] ChrX:21992629 [GRCh38]
ChrX:22010747 [GRCh37]
ChrX:Xp22.11
likely benign|conflicting interpretations of pathogenicity|uncertain significance
GRCh38/hg38 Xp22.33-q28(chrX:10701-155978689)x1 copy number loss See cases [RCV000133792] ChrX:10701..155978689 [GRCh38]
ChrX:60701..155208354 [GRCh37]
ChrX:701..154861548 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-11.22(chrX:10701-52857805)x1 copy number loss See cases [RCV000133817] ChrX:10701..52857805 [GRCh38]
ChrX:60701..52886834 [GRCh37]
ChrX:701..52903559 [NCBI36]
ChrX:Xp22.33-11.22
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:10679-156013167)x3 copy number gain See cases [RCV000050385] ChrX:10679..156013167 [GRCh38]
ChrX:60679..155242832 [GRCh37]
ChrX:679..154896026 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:10679-156013167)x1 copy number loss See cases [RCV000050386] ChrX:10679..156013167 [GRCh38]
ChrX:60679..155242832 [GRCh37]
ChrX:679..154896026 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:14245-155999293)x1 copy number loss See cases [RCV000052982] ChrX:14245..155999293 [GRCh38]
ChrX:64245..155228958 [GRCh37]
ChrX:4245..154882152 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:26102-155996431)x3 copy number gain See cases [RCV000052984] ChrX:26102..155996431 [GRCh38]
ChrX:76102..155226096 [GRCh37]
ChrX:16102..154879290 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:26102-155996431)x1 copy number loss See cases [RCV000052986] ChrX:26102..155996431 [GRCh38]
ChrX:76102..155226096 [GRCh37]
ChrX:16102..154879290 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-11.23(chrX:10679-50059388)x1 copy number loss See cases [RCV000133745] ChrX:10679..50059388 [GRCh38]
ChrX:60679..49824045 [GRCh37]
ChrX:679..49710785 [NCBI36]
ChrX:Xp22.33-11.23
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:20297-155999253)x3 copy number gain See cases [RCV000134564] ChrX:20297..155999253 [GRCh38]
ChrX:70297..155228918 [GRCh37]
ChrX:10297..154882112 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q11.1(chrX:10701-62712219)x1 copy number loss See cases [RCV000134568] ChrX:10701..62712219 [GRCh38]
ChrX:60701..61931689 [GRCh37]
ChrX:701..61848414 [NCBI36]
ChrX:Xp22.33-q11.1
pathogenic
GRCh38/hg38 Xp22.33-11.21(chrX:10701-58055053)x1 copy number loss See cases [RCV000134026] ChrX:10701..58055053 [GRCh38]
ChrX:60701..58081487 [GRCh37]
ChrX:701..58098212 [NCBI36]
ChrX:Xp22.33-11.21
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:10701-156003242)x1 copy number loss See cases [RCV000133947] ChrX:10701..156003242 [GRCh38]
ChrX:60701..155232907 [GRCh37]
ChrX:701..154886101 [NCBI36]
ChrX:Xp22.33-q28
pathogenic|conflicting interpretations of pathogenicity|conflicting data from submitters
GRCh38/hg38 Xp22.33-q28(chrX:10701-156003242)x3 copy number gain See cases [RCV000133911] ChrX:10701..156003242 [GRCh38]
ChrX:60701..155232907 [GRCh37]
ChrX:701..154886101 [NCBI36]
ChrX:Xp22.33-q28
pathogenic|likely pathogenic|conflicting data from submitters
GRCh38/hg38 Xp22.31-11.22(chrX:8176030-53962833)x1 copy number loss See cases [RCV000135305] ChrX:8176030..53962833 [GRCh38]
ChrX:8144071..53989266 [GRCh37]
ChrX:8104071..54005991 [NCBI36]
ChrX:Xp22.31-11.22
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:20297-156026127)x1 copy number loss See cases [RCV000135321] ChrX:20297..156026127 [GRCh38]
ChrX:70297..155255792 [GRCh37]
ChrX:10297..154908986 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-21.1(chrX:233335-37292980)x1 copy number loss See cases [RCV000135299] ChrX:233335..37292980 [GRCh38]
ChrX:150002..37152232 [GRCh37]
ChrX:90002..37037153 [NCBI36]
ChrX:Xp22.33-21.1
pathogenic
GRCh38/hg38 Xp22.2-22.11(chrX:15173626-23952585)x2 copy number gain See cases [RCV000134875] ChrX:15173626..23952585 [GRCh38]
ChrX:15191748..23970702 [GRCh37]
ChrX:15101669..23880623 [NCBI36]
ChrX:Xp22.2-22.11
pathogenic
GRCh38/hg38 Xp22.33-11.22(chrX:10679-52857805)x3 copy number gain See cases [RCV000134957] ChrX:10679..52857805 [GRCh38]
ChrX:60679..52886834 [GRCh37]
ChrX:679..52903559 [NCBI36]
ChrX:Xp22.33-11.22
pathogenic
GRCh38/hg38 Xp22.33-21.1(chrX:10679-36186635)x1 copy number loss See cases [RCV000135551] ChrX:10679..36186635 [GRCh38]
ChrX:60679..36202463 [GRCh37]
ChrX:679..36114673 [NCBI36]
ChrX:Xp22.33-21.1
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:10701-156003229)x1 copy number loss See cases [RCV000136097] ChrX:10701..156003229 [GRCh38]
ChrX:60701..155232894 [GRCh37]
ChrX:701..154886088 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:40904-155998166)x1 copy number loss See cases [RCV000136478] ChrX:40904..155998166 [GRCh38]
ChrX:90904..155227831 [GRCh37]
ChrX:30904..154881025 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q25(chrX:10701-128393708) copy number loss See cases [RCV000136094] ChrX:10701..128393708 [GRCh38]
ChrX:60701..127527686 [GRCh37]
ChrX:701..127355367 [NCBI36]
ChrX:Xp22.33-q25
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:10001-156030895)x1 copy number loss See cases [RCV000136005] ChrX:10001..156030895 [GRCh38]
ChrX:60001..155260560 [GRCh37]
ChrX:1..154913754 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q13.3(chrX:10679-76420505)x3 copy number gain See cases [RCV000137137] ChrX:10679..76420505 [GRCh38]
ChrX:60679..75640898 [GRCh37]
ChrX:679..75557302 [NCBI36]
ChrX:Xp22.33-q13.3
pathogenic|likely benign
GRCh38/hg38 Xp22.33-11.22(chrX:10679-52213731)x1 copy number loss See cases [RCV000137112] ChrX:10679..52213731 [GRCh38]
ChrX:60679..51948998 [GRCh37]
ChrX:679..51973598 [NCBI36]
ChrX:Xp22.33-11.22
pathogenic|uncertain significance
GRCh38/hg38 Xp22.33-q28(chrX:2782275-155611794)x2 copy number gain See cases [RCV000136841] ChrX:2782275..155611794 [GRCh38]
ChrX:2700316..154785891 [GRCh37]
ChrX:2710316..154494649 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:2765636-155522304)x3 copy number gain See cases [RCV000136791] ChrX:2765636..155522304 [GRCh38]
ChrX:2683677..154751965 [GRCh37]
ChrX:2693677..154405159 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-11.22(chrX:10701-52033734)x1 copy number loss See cases [RCV000137430] ChrX:10701..52033734 [GRCh38]
ChrX:60701..51776830 [GRCh37]
ChrX:701..51793570 [NCBI36]
ChrX:Xp22.33-11.22
pathogenic
GRCh38/hg38 Xp22.33-11.21(chrX:10701-58055036)x1 copy number loss See cases [RCV000137552] ChrX:10701..58055036 [GRCh38]
ChrX:60701..58081470 [GRCh37]
ChrX:701..58098195 [NCBI36]
ChrX:Xp22.33-11.21
pathogenic
GRCh38/hg38 Xp22.33-11.23(chrX:10679-49157514)x1 copy number loss See cases [RCV000137166] ChrX:10679..49157514 [GRCh38]
ChrX:60679..49016667 [GRCh37]
ChrX:679..48903611 [NCBI36]
ChrX:Xp22.33-11.23
pathogenic
GRCh38/hg38 Xp22.33-11.23(chrX:10701-49071220)x1 copy number loss See cases [RCV000137413] ChrX:10701..49071220 [GRCh38]
ChrX:60701..48928877 [GRCh37]
ChrX:701..48815821 [NCBI36]
ChrX:Xp22.33-11.23
pathogenic
GRCh38/hg38 Xp22.2-21.2(chrX:12254555-30410580)x1 copy number loss See cases [RCV000138069] ChrX:12254555..30410580 [GRCh38]
ChrX:12272674..30428697 [GRCh37]
ChrX:12182595..30338618 [NCBI36]
ChrX:Xp22.2-21.2
pathogenic|likely pathogenic
GRCh38/hg38 Xp22.33-21.1(chrX:10701-37723318)x1 copy number loss See cases [RCV000138019] ChrX:10701..37723318 [GRCh38]
ChrX:60701..37318587 [GRCh37]
ChrX:701..37467510 [NCBI36]
ChrX:Xp22.33-21.1
pathogenic
GRCh38/hg38 Xp22.33-q22.3(chrX:10701-106113403)x1 copy number loss See cases [RCV000137886] ChrX:10701..106113403 [GRCh38]
ChrX:60701..105357395 [GRCh37]
ChrX:701..105244051 [NCBI36]
ChrX:Xp22.33-q22.3
pathogenic
GRCh38/hg38 Xp22.2-q27.3(chrX:13020141-143473520)x1 copy number loss See cases [RCV000138678] ChrX:13020141..143473520 [GRCh38]
ChrX:13038260..142561303 [GRCh37]
ChrX:12948181..142388969 [NCBI36]
ChrX:Xp22.2-q27.3
pathogenic
GRCh38/hg38 Xp22.33-11.1(chrX:10701-58517661)x1 copy number loss See cases [RCV000139343] ChrX:10701..58517661 [GRCh38]
ChrX:60701..58544094 [GRCh37]
ChrX:701..58560819 [NCBI36]
ChrX:Xp22.33-11.1
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:1085618-155699644)x1 copy number loss See cases [RCV000139278] ChrX:1085618..155699644 [GRCh38]
ChrX:1118268..154929305 [GRCh37]
ChrX:1038268..154582499 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q21.31(chrX:10701-88318651)x1 copy number loss See cases [RCV000139352] ChrX:10701..88318651 [GRCh38]
ChrX:60701..87573652 [GRCh37]
ChrX:701..87460308 [NCBI36]
ChrX:Xp22.33-q21.31
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:251880-156004181)x3 copy number gain See cases [RCV000139888] ChrX:251880..156004181 [GRCh38]
ChrX:168547..155233846 [GRCh37]
ChrX:108547..154887040 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-11.4(chrX:3909315-38682287)x3 copy number gain See cases [RCV000141261] ChrX:3909315..38682287 [GRCh38]
ChrX:3827356..38541541 [GRCh37]
ChrX:3837356..38426485 [NCBI36]
ChrX:Xp22.33-11.4
uncertain significance
GRCh38/hg38 Xp22.33-q28(chrX:2299223-155992188)x3 copy number gain See cases [RCV000141400] ChrX:2299223..155992188 [GRCh38]
ChrX:2217264..155221853 [GRCh37]
ChrX:2227264..154875047 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:20297-156016920)x3 copy number gain See cases [RCV000141401] ChrX:20297..156016920 [GRCh38]
ChrX:70297..155246585 [GRCh37]
ChrX:10297..154899779 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:251880-156004066)x4 copy number gain See cases [RCV000140786] ChrX:251880..156004066 [GRCh38]
ChrX:168547..155233731 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-11.22(chrX:10701-53750424)x1 copy number loss See cases [RCV000140711] ChrX:10701..53750424 [GRCh38]
ChrX:60701..53776922 [GRCh37]
ChrX:701..53793647 [NCBI36]
ChrX:Xp22.33-11.22
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:251880-156004066)x1 copy number loss See cases [RCV000140787] ChrX:251880..156004066 [GRCh38]
ChrX:168547..155233731 [GRCh37]
ChrX:Xp22.33-q28
pathogenic|conflicting data from submitters
GRCh38/hg38 Xp22.33-11.22(chrX:251879-50289363)x1 copy number loss See cases [RCV000141741] ChrX:251879..50289363 [GRCh38]
ChrX:168546..50032363 [GRCh37]
ChrX:108546..50049103 [NCBI36]
ChrX:Xp22.33-11.22
pathogenic
GRCh38/hg38 Xp22.33-q12(chrX:251880-66445845)x1 copy number loss See cases [RCV000142334] ChrX:251880..66445845 [GRCh38]
ChrX:168547..65665687 [GRCh37]
ChrX:108547..65582412 [NCBI36]
ChrX:Xp22.33-q12
pathogenic
GRCh38/hg38 Xp22.33-11.22(chrX:251880-51643625)x1 copy number loss See cases [RCV000142035] ChrX:251880..51643625 [GRCh38]
ChrX:168547..51386559 [GRCh37]
ChrX:108547..51403299 [NCBI36]
ChrX:Xp22.33-11.22
pathogenic
GRCh38/hg38 Xp22.33-q24(chrX:251879-118847157)x3 copy number gain See cases [RCV000142134] ChrX:251879..118847157 [GRCh38]
ChrX:168546..117981120 [GRCh37]
ChrX:108546..117865148 [NCBI36]
ChrX:Xp22.33-q24
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:10701-156003229)x3 copy number gain See cases [RCV000142625] ChrX:10701..156003229 [GRCh38]
ChrX:60701..155232894 [GRCh37]
ChrX:701..154886088 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:251879-156004066)x1 copy number loss See cases [RCV000143441] ChrX:251879..156004066 [GRCh38]
ChrX:168546..155233731 [GRCh37]
ChrX:108546..154886925 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:251879-156004066)x3 copy number gain See cases [RCV000143433] ChrX:251879..156004066 [GRCh38]
ChrX:168546..155233731 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-11.22(chrX:10701-53131191)x1 copy number loss See cases [RCV000143348] ChrX:10701..53131191 [GRCh38]
ChrX:60701..53047381 [GRCh37]
ChrX:701..53177098 [NCBI36]
ChrX:Xp22.33-11.22
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:251880-156004066)x3 copy number gain See cases [RCV000143219] ChrX:251880..156004066 [GRCh38]
ChrX:168547..155233731 [GRCh37]
ChrX:108547..154886925 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-11.21(chrX:251879-56428859)x1 copy number loss See cases [RCV000143130] ChrX:251879..56428859 [GRCh38]
ChrX:168546..56455292 [GRCh37]
ChrX:108546..56472017 [NCBI36]
ChrX:Xp22.33-11.21
pathogenic
GRCh38/hg38 Xp22.33-21.1(chrX:251879-35885004)x1 copy number loss See cases [RCV000143496] ChrX:251879..35885004 [GRCh38]
ChrX:168546..35903121 [GRCh37]
ChrX:108546..35813042 [NCBI36]
ChrX:Xp22.33-21.1
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:10679-156022206)x3 copy number gain See cases [RCV000148141] ChrX:10679..156022206 [GRCh38]
ChrX:60679..155251871 [GRCh37]
ChrX:679..154905065 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
GRCh38/hg38 Xp22.33-q28(chrX:10679-156022206)x1 copy number loss See cases [RCV000148135] ChrX:10679..156022206 [GRCh38]
ChrX:60679..155251871 [GRCh37]
ChrX:679..154905065 [NCBI36]
ChrX:Xp22.33-q28
pathogenic
NM_004595.5(SMS):c.330A>G (p.Arg110=) single nucleotide variant not specified [RCV000192724] ChrX:21977061 [GRCh38]
ChrX:21995179 [GRCh37]
ChrX:Xp22.11
uncertain significance
NM_004595.5(SMS):c.714C>T (p.Gly238=) single nucleotide variant History of neurodevelopmental disorder [RCV000717166]|not specified [RCV000194134] ChrX:21978930 [GRCh38]
ChrX:21997048 [GRCh37]
ChrX:Xp22.11
likely benign|uncertain significance
NM_004595.5(SMS):c.699G>A (p.Met233Ile) single nucleotide variant not provided [RCV000179890] ChrX:21978915 [GRCh38]
ChrX:21997033 [GRCh37]
ChrX:Xp22.11
uncertain significance
NM_004595.5(SMS):c.661-5C>T single nucleotide variant not provided [RCV000179891] ChrX:21978872 [GRCh38]
ChrX:21996990 [GRCh37]
ChrX:Xp22.11
conflicting interpretations of pathogenicity|uncertain significance
GRCh37/hg19 Xp22.33-q28(chrX:71267-155246643)x3 copy number gain See cases [RCV000240122] ChrX:71267..155246643 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:176426-155250222)x3 copy number gain See cases [RCV000239843] ChrX:176426..155250222 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.2-q28(chrX:13147668-155250222)x3 copy number gain See cases [RCV000239798] ChrX:13147668..155250222 [GRCh37]
ChrX:Xp22.2-q28
pathogenic
GRCh37/hg19 Xp22.33-11.21(chrX:70297-58066465)x1 copy number loss See cases [RCV000239814] ChrX:70297..58066465 [GRCh37]
ChrX:Xp22.33-11.21
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:71267-155255839)x1 copy number loss See cases [RCV000239832] ChrX:71267..155255839 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:553069-155233731)x1 copy number loss See cases [RCV000446026] ChrX:553069..155233731 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:70297-155255839)x3 copy number gain See cases [RCV000239934] ChrX:70297..155255839 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:150002-155234036)x2 copy number gain See cases [RCV000240106] ChrX:150002..155234036 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:71267-155224766)x1 copy number loss See cases [RCV000239902] ChrX:71267..155224766 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:60701-155246271)x3 copy number gain See cases [RCV000239989] ChrX:60701..155246271 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:71267-155234036)x2 copy number gain See cases [RCV000239874] ChrX:71267..155234036 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:176426-155236656)x3 copy number gain See cases [RCV000240552] ChrX:176426..155236656 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:150002-155234036)x3 copy number gain See cases [RCV000240314] ChrX:150002..155234036 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:225816-155234036)x2 copy number gain See cases [RCV000240464] ChrX:225816..155234036 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-21.1(chrX:71267-35809046)x1 copy number loss See cases [RCV000240335] ChrX:71267..35809046 [GRCh37]
ChrX:Xp22.33-21.1
pathogenic
GRCh37/hg19 Xp22.33-21.3(chrX:1378591-25940311)x2 copy number gain See cases [RCV000240441] ChrX:1378591..25940311 [GRCh37]
ChrX:Xp22.33-21.3
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:2707626-155250222)x2 copy number gain See cases [RCV000240541] ChrX:2707626..155250222 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.2-q25(chrX:11692290-121187337)x2 copy number gain not provided [RCV000488046] ChrX:11692290..121187337 [GRCh37]
ChrX:Xp22.2-q25
uncertain significance
NM_004595.5(SMS):c.638C>A (p.Pro213Gln) single nucleotide variant Inborn genetic diseases [RCV000622379] ChrX:21978092 [GRCh38]
ChrX:21996210 [GRCh37]
ChrX:Xp22.11
uncertain significance
Single allele duplication Syndromic X-linked intellectual disability Lubs type [RCV000768455] ChrX:15323210..153542100 [GRCh37]
ChrX:Xp22.2-q28
pathogenic
GRCh37/hg19 Xp22.33-11.23(chrX:60814-48317386)x1 copy number loss not provided [RCV000753273] ChrX:60814..48317386 [GRCh37]
ChrX:Xp22.33-11.23
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:168546-154930047)x3 copy number gain See cases [RCV000449437] ChrX:168546..154930047 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:168546-155233731)x3 copy number gain See cases [RCV000449330] ChrX:168546..155233731 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-11.3(chrX:168546-43917011)x3 copy number gain See cases [RCV000449393] ChrX:168546..43917011 [GRCh37]
ChrX:Xp22.33-11.3
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:70297-155255792) copy number loss See cases [RCV000449461] ChrX:70297..155255792 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-11.21(chrX:168546-55529093)x1 copy number loss See cases [RCV000446584] ChrX:168546..55529093 [GRCh37]
ChrX:Xp22.33-11.21
pathogenic
GRCh37/hg19 Xp22.33-11.21(chrX:168546-56684082)x1 copy number loss See cases [RCV000447092] ChrX:168546..56684082 [GRCh37]
ChrX:Xp22.33-11.21
pathogenic
GRCh37/hg19 Xp22.33-11.22(chrX:168546-52573789)x1 copy number loss See cases [RCV000447470] ChrX:168546..52573789 [GRCh37]
ChrX:Xp22.33-11.22
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:2703632-155233731)x1 copy number loss See cases [RCV000446712] ChrX:2703632..155233731 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:71267-155255792)x1 copy number loss See cases [RCV000446197] ChrX:71267..155255792 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:60701-155246225)x3 copy number gain See cases [RCV000446270] ChrX:60701..155246225 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:318707-155224707)x1 copy number loss See cases [RCV000446667] ChrX:318707..155224707 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:168546-155233731)x4 copy number gain See cases [RCV000446932] ChrX:168546..155233731 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:168546-155196888)x3 copy number gain See cases [RCV000446310] ChrX:168546..155196888 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:168546-155081533)x3 copy number gain See cases [RCV000447253] ChrX:168546..155081533 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
NM_004595.5(SMS):c.661-4G>T single nucleotide variant not specified [RCV000417669] ChrX:21978873 [GRCh38]
ChrX:21996991 [GRCh37]
ChrX:Xp22.11
likely benign
GRCh37/hg19 Xp22.33-q28(chrX:168566-155233731)x1 copy number loss See cases [RCV000445720] ChrX:168566..155233731 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:168546-155233731)x1 copy number loss See cases [RCV000448393] ChrX:168546..155233731 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:70297-155255792)x4 copy number gain See cases [RCV000448034] ChrX:70297..155255792 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-11.1(chrX:168546-58140271)x1 copy number loss See cases [RCV000447773] ChrX:168546..58140271 [GRCh37]
ChrX:Xp22.33-11.1
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:70297-155246585)x1 copy number loss See cases [RCV000448652] ChrX:70297..155246585 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.12-22.11(chrX:21708594-22063592)x2 copy number gain See cases [RCV000512061] ChrX:21708594..22063592 [GRCh37]
ChrX:Xp22.12-22.11
uncertain significance
NM_004595.5(SMS):c.831G>T (p.Leu277Phe) single nucleotide variant not provided [RCV000480904] ChrX:21984384 [GRCh38]
ChrX:22002502 [GRCh37]
ChrX:Xp22.11
likely pathogenic
GRCh37/hg19 Xp22.33-11.21(chrX:168546-55240087)x1 copy number loss See cases [RCV000512136] ChrX:168546..55240087 [GRCh37]
ChrX:Xp22.33-11.21
pathogenic
GRCh37/hg19 Xp22.33-11.1(chrX:168546-58527164)x1 copy number loss See cases [RCV000510437] ChrX:168546..58527164 [GRCh37]
ChrX:Xp22.33-11.1
pathogenic
GRCh37/hg19 Xp22.33-21.1(chrX:168546-37515849)x1 copy number loss See cases [RCV000510590] ChrX:168546..37515849 [GRCh37]
ChrX:Xp22.33-21.1
pathogenic
NM_004595.5(SMS):c.665A>T (p.Asp222Val) single nucleotide variant SMS-Related Disorder [RCV000509103]|not provided [RCV000522772] ChrX:21978881 [GRCh38]
ChrX:21996999 [GRCh37]
ChrX:Xp22.11
likely pathogenic|not provided
GRCh37/hg19 Xp22.33-q28(chrX:168547-151304063)x1 copy number loss See cases [RCV000510382] ChrX:168547..151304063 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-21.1(chrX:168546-35841052)x1 copy number loss See cases [RCV000510308] ChrX:168546..35841052 [GRCh37]
ChrX:Xp22.33-21.1
pathogenic
GRCh37/hg19 Xp22.33-q23(chrX:168547-112474026)x1 copy number loss See cases [RCV000510419] ChrX:168547..112474026 [GRCh37]
ChrX:Xp22.33-q23
pathogenic
GRCh37/hg19 Xp22.33-11.21(chrX:168546-57504183)x1 copy number loss See cases [RCV000511615] ChrX:168546..57504183 [GRCh37]
ChrX:Xp22.33-11.21
pathogenic
GRCh37/hg19 Xp22.33-11.21(chrX:168546-57683964)x1 copy number loss See cases [RCV000512022] ChrX:168546..57683964 [GRCh37]
ChrX:Xp22.33-11.21
pathogenic
GRCh37/hg19 Xp22.33-21.2(chrX:168546-31085327)x1 copy number loss See cases [RCV000511350] ChrX:168546..31085327 [GRCh37]
ChrX:Xp22.33-21.2
pathogenic
GRCh37/hg19 Xp22.2-21.2(chrX:15290524-29747172)x2 copy number gain See cases [RCV000511443] ChrX:15290524..29747172 [GRCh37]
ChrX:Xp22.2-21.2
likely pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:168547-155233731) copy number gain See cases [RCV000512020] ChrX:168547..155233731 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.12-22.11(chrX:21708594-22054641)x3 copy number gain See cases [RCV000511611] ChrX:21708594..22054641 [GRCh37]
ChrX:Xp22.12-22.11
uncertain significance
GRCh37/hg19 Xp22.33-11.21(chrX:168546-54996659)x1 copy number loss See cases [RCV000510822] ChrX:168546..54996659 [GRCh37]
ChrX:Xp22.33-11.21
pathogenic
GRCh37/hg19 Xp22.33-22.11(chrX:168546-24780527)x3 copy number gain See cases [RCV000512204] ChrX:168546..24780527 [GRCh37]
ChrX:Xp22.33-22.11
pathogenic
GRCh37/hg19 Xp22.33-q13.3(chrX:168546-74549686) copy number loss See cases [RCV000512142] ChrX:168546..74549686 [GRCh37]
ChrX:Xp22.33-q13.3
pathogenic
GRCh37/hg19 Xp22.33-11.21(chrX:168564-57413442)x1 copy number loss See cases [RCV000512339] ChrX:168564..57413442 [GRCh37]
ChrX:Xp22.33-11.21
pathogenic
NM_004595.5(SMS):c.820A>G (p.Ile274Val) single nucleotide variant History of neurodevelopmental disorder [RCV000716920] ChrX:21984373 [GRCh38]
ChrX:22002491 [GRCh37]
ChrX:Xp22.11
uncertain significance
GRCh37/hg19 Xp22.33-11.23(chrX:168546-46908284)x1 copy number loss not provided [RCV000684185] ChrX:168546..46908284 [GRCh37]
ChrX:Xp22.33-11.23
pathogenic
GRCh37/hg19 Xp22.31-q21.31(chrX:7841947-90815333)x1,2 copy number gain not provided [RCV000684261] ChrX:7841947..90815333 [GRCh37]
ChrX:Xp22.31-q21.31
pathogenic
GRCh37/hg19 Xp22.33-22.11(chrX:168546-23785738)x1 copy number loss not provided [RCV000684183] ChrX:168546..23785738 [GRCh37]
ChrX:Xp22.33-22.11
pathogenic
GRCh37/hg19 Xp22.33-11.3(chrX:168546-43248706)x1 copy number loss not provided [RCV000684184] ChrX:168546..43248706 [GRCh37]
ChrX:Xp22.33-11.3
pathogenic
GRCh37/hg19 Xp22.33-11.22(chrX:60814-51821765)x1 copy number loss not provided [RCV000753274] ChrX:60814..51821765 [GRCh37]
ChrX:Xp22.33-11.22
pathogenic
GRCh37/hg19 Xp22.33-11.21(chrX:60814-55476165)x1 copy number loss not provided [RCV000753275] ChrX:60814..55476165 [GRCh37]
ChrX:Xp22.33-11.21
pathogenic
NM_004595.5(SMS):c.789C>T (p.Tyr263=) single nucleotide variant History of neurodevelopmental disorder [RCV000718024] ChrX:21984342 [GRCh38]
ChrX:22002460 [GRCh37]
ChrX:Xp22.11
likely benign
NM_004595.5(SMS):c.114G>A (p.Ser38=) single nucleotide variant History of neurodevelopmental disorder [RCV000718959]|not provided [RCV000934691] ChrX:21967260 [GRCh38]
ChrX:21985378 [GRCh37]
ChrX:Xp22.11
likely benign
NM_004595.5(SMS):c.561A>G (p.Glu187=) single nucleotide variant History of neurodevelopmental disorder [RCV000721049]|not provided [RCV000918745] ChrX:21978015 [GRCh38]
ChrX:21996133 [GRCh37]
ChrX:Xp22.11
benign
NM_004595.5(SMS):c.505+3A>G single nucleotide variant History of neurodevelopmental disorder [RCV000720966]|not provided [RCV001302433] ChrX:21977239 [GRCh38]
ChrX:21995357 [GRCh37]
ChrX:Xp22.11
uncertain significance
Single allele duplication Autistic disorder of childhood onset [RCV000754365] ChrX:1..156040895 [GRCh38]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:60262-155245765)x1 copy number loss not provided [RCV000753271] ChrX:60262..155245765 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
Single allele duplication Autistic disorder of childhood onset [RCV000754363] ChrX:10000..22474705 [GRCh38]
ChrX:Xp22.33-22.11
likely pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:60814-155254881)x2 copy number gain not provided [RCV000753277] ChrX:60814..155254881 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:60262-155245765)x3 copy number gain not provided [RCV000753272] ChrX:60262..155245765 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:181779-155171702)x1 copy number loss not provided [RCV000753278] ChrX:181779..155171702 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:60814-155236712)x2 copy number gain not provided [RCV000753276] ChrX:60814..155236712 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
NM_004595.5(SMS):c.581T>G (p.Val194Gly) single nucleotide variant Smith-Magenis syndrome [RCV000760247] ChrX:21978035 [GRCh38]
ChrX:21996153 [GRCh37]
ChrX:Xp22.11
likely pathogenic
GRCh37/hg19 Xp22.11(chrX:21956780-21977221)x1 copy number loss not provided [RCV001007273] ChrX:21956780..21977221 [GRCh37]
ChrX:Xp22.11
uncertain significance
Single allele deletion Neurodevelopmental disorder [RCV000787440] ChrX:1..47140860 [GRCh37]
ChrX:Xp22.33-11.23
pathogenic
NM_004595.5(SMS):c.171C>T (p.Ser57=) single nucleotide variant not provided [RCV000902528] ChrX:21971897 [GRCh38]
ChrX:21990015 [GRCh37]
ChrX:Xp22.11
benign
NC_000023.10:g.(?_21990015)_(22292386_?)del deletion not provided [RCV001031815] ChrX:21990015..22292386 [GRCh37]
ChrX:Xp22.11
pathogenic
GRCh37/hg19 Xp22.33-22.11(chrX:801301-23768392) copy number gain not provided [RCV000767802] ChrX:801301..23768392 [GRCh37]
ChrX:Xp22.33-22.11
pathogenic
GRCh37/hg19 Xp22.33-11.22(chrX:60814-50519984)x1 copy number loss See cases [RCV000790583] ChrX:60814..50519984 [GRCh37]
ChrX:Xp22.33-11.22
pathogenic
NM_004595.5(SMS):c.45C>G (p.Ala15=) single nucleotide variant not provided [RCV000975280] ChrX:21940869 [GRCh38]
ChrX:21958987 [GRCh37]
ChrX:Xp22.11
likely benign
GRCh37/hg19 Xp22.33-11.4(chrX:168546-38054739)x1 copy number loss not provided [RCV000845671] ChrX:168546..38054739 [GRCh37]
ChrX:Xp22.33-11.4
pathogenic
GRCh37/hg19 Xp22.2-22.11(chrX:13962918-22148232)x2 copy number gain not provided [RCV000849766] ChrX:13962918..22148232 [GRCh37]
ChrX:Xp22.2-22.11
pathogenic
GRCh37/hg19 Xp22.2-22.11(chrX:13962918-22148232)x2 copy number gain not provided [RCV000849768] ChrX:13962918..22148232 [GRCh37]
ChrX:Xp22.2-22.11
pathogenic
NM_004595.5(SMS):c.388C>T (p.Arg130Cys) single nucleotide variant Syndromic X-linked intellectual disability Snyder type [RCV001007564] ChrX:21977119 [GRCh38]
ChrX:21995237 [GRCh37]
ChrX:Xp22.11
pathogenic
GRCh37/hg19 Xp22.33-q11.1(chrX:168546-61877279)x1 copy number loss not provided [RCV000846273] ChrX:168546..61877279 [GRCh37]
ChrX:Xp22.33-q11.1
pathogenic
GRCh37/hg19 Xp22.11(chrX:21999106-22054641)x2 copy number gain not provided [RCV000846248] ChrX:21999106..22054641 [GRCh37]
ChrX:Xp22.11
uncertain significance
GRCh37/hg19 Xp22.11(chrX:21999106-22054641)x2 copy number gain not provided [RCV000846605] ChrX:21999106..22054641 [GRCh37]
ChrX:Xp22.11
uncertain significance
GRCh37/hg19 Xp22.12-21.1(chrX:20925922-35511818)x1 copy number loss not provided [RCV000847678] ChrX:20925922..35511818 [GRCh37]
ChrX:Xp22.12-21.1
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:168546-155233731)x1 copy number loss not provided [RCV000848828] ChrX:168546..155233731 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp22.33-22.11(chrX:2190434-23795839)x3 copy number gain not provided [RCV000849574] ChrX:2190434..23795839 [GRCh37]
ChrX:Xp22.33-22.11
pathogenic
GRCh37/hg19 Xp22.33-21.1(chrX:168546-34753512)x1 copy number loss not provided [RCV001007559] ChrX:168546..34753512 [GRCh37]
ChrX:Xp22.33-21.1
pathogenic
GRCh37/hg19 Xp22.33-22.11(chrX:537158-22883547)x1 copy number loss not provided [RCV001007223] ChrX:537158..22883547 [GRCh37]
ChrX:Xp22.33-22.11
pathogenic
GRCh37/hg19 Xp22.33-11.21(chrX:539722-55509385)x1 copy number loss not provided [RCV001007224] ChrX:539722..55509385 [GRCh37]
ChrX:Xp22.33-11.21
pathogenic
NM_004595.5(SMS):c.799G>A (p.Gly267Arg) single nucleotide variant Syndromic X-linked intellectual disability Snyder type [RCV000985012] ChrX:21984352 [GRCh38]
ChrX:22002470 [GRCh37]
ChrX:Xp22.11
uncertain significance
GRCh37/hg19 Xp22.11(chrX:21999106-22054641)x2 copy number gain not provided [RCV000846247] ChrX:21999106..22054641 [GRCh37]
ChrX:Xp22.11
uncertain significance
GRCh37/hg19 Xp22.33-q28(chrX:168546-155233731)x4 copy number gain not provided [RCV000846039] ChrX:168546..155233731 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
NM_004595.5(SMS):c.328C>G (p.Arg110Gly) single nucleotide variant Syndromic X-linked intellectual disability Snyder type [RCV001250132] ChrX:21972570 [GRCh38]
ChrX:21990688 [GRCh37]
ChrX:Xp22.11
likely pathogenic
NM_004595.5(SMS):c.908_911del (p.Met303fs) deletion Syndromic X-linked intellectual disability Snyder type [RCV000853623] ChrX:21985184..21985187 [GRCh38]
ChrX:22003302..22003305 [GRCh37]
ChrX:Xp22.11
pathogenic
NM_004595.5(SMS):c.63C>T (p.Thr21=) single nucleotide variant not provided [RCV000976024] ChrX:21967209 [GRCh38]
ChrX:21985327 [GRCh37]
ChrX:Xp22.11
benign
NM_004595.5(SMS):c.13C>G (p.Arg5Gly) single nucleotide variant Syndromic X-linked intellectual disability Snyder type [RCV001169877] ChrX:21940837 [GRCh38]
ChrX:21958955 [GRCh37]
ChrX:Xp22.11
uncertain significance
NC_000023.11:g.(?_21977061)_(22077702_?)del deletion not provided [RCV001031635] ChrX:21995179..22095820 [GRCh37]
ChrX:Xp22.11
pathogenic
NM_004595.5(SMS):c.3G>A (p.Met1Ile) single nucleotide variant not provided [RCV000999350] ChrX:21940827 [GRCh38]
ChrX:21958945 [GRCh37]
ChrX:Xp22.11
uncertain significance
NM_004595.5(SMS):c.410A>G (p.Asp137Gly) single nucleotide variant Syndromic X-linked intellectual disability Snyder type [RCV001171510] ChrX:21977141 [GRCh38]
ChrX:21995259 [GRCh37]
ChrX:Xp22.11
likely pathogenic
NM_004595.5(SMS):c.905C>T (p.Ser302Leu) single nucleotide variant Intellectual disability [RCV001249470] ChrX:21985183 [GRCh38]
ChrX:22003301 [GRCh37]
ChrX:Xp22.11
pathogenic
NM_004595.5(SMS):c.844A>G (p.Ile282Val) single nucleotide variant not provided [RCV001041036] ChrX:21984397 [GRCh38]
ChrX:22002515 [GRCh37]
ChrX:Xp22.11
uncertain significance
NM_004595.5(SMS):c.872C>A (p.Thr291Lys) single nucleotide variant Syndromic X-linked intellectual disability Snyder type [RCV001197950] ChrX:21985150 [GRCh38]
ChrX:22003268 [GRCh37]
ChrX:Xp22.11
uncertain significance
GRCh37/hg19 Xp22.33-11.21(chrX:219609-55466476)x1 copy number loss See cases [RCV001263061] ChrX:219609..55466476 [GRCh37]
ChrX:Xp22.33-11.21
pathogenic
NM_004595.5(SMS):c.608G>A (p.Gly203Asp) single nucleotide variant Syndromic X-linked intellectual disability Snyder type [RCV001255181] ChrX:21978062 [GRCh38]
ChrX:21996180 [GRCh37]
ChrX:Xp22.11
pathogenic
NM_004595.5(SMS):c.1019A>G (p.Glu340Gly) single nucleotide variant Syndromic X-linked intellectual disability Snyder type [RCV001329289] ChrX:21992670 [GRCh38]
ChrX:22010788 [GRCh37]
ChrX:Xp22.11
uncertain significance
NM_004595.5(SMS):c.350G>T (p.Gly117Val) single nucleotide variant not provided [RCV001311824] ChrX:21977081 [GRCh38]
ChrX:21995199 [GRCh37]
ChrX:Xp22.11
likely pathogenic
GRCh37/hg19 Xp22.33-11.21(chrX:168546-56457794)x1 copy number loss not provided [RCV001281358] ChrX:168546..56457794 [GRCh37]
ChrX:Xp22.33-11.21
pathogenic
NM_004595.5(SMS):c.587T>C (p.Ile196Thr) single nucleotide variant Syndromic X-linked intellectual disability Snyder type [RCV001310252] ChrX:21978041 [GRCh38]
ChrX:21996159 [GRCh37]
ChrX:Xp22.11
likely pathogenic
NM_004595.5(SMS):c.330-10C>G single nucleotide variant not provided [RCV001289229] ChrX:21977051 [GRCh38]
ChrX:21995169 [GRCh37]
ChrX:Xp22.11
uncertain significance

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:11123 AgrOrtholog
COSMIC SMS COSMIC
Ensembl Genes ENSG00000102172 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000368714 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000385746 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000407366 UniProtKB/TrEMBL
Ensembl Transcript ENST00000379404 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000404933 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000457085 UniProtKB/TrEMBL
Gene3D-CATH 2.30.140.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.160.110 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000102172 GTEx
HGNC ID HGNC:11123 ENTREZGENE
Human Proteome Map SMS Human Proteome Map
InterPro PABS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PABS_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAM-dependent_MTases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sirohaem_synthase-like_central UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Spermidine_synt_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Spermidine_synt_N_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Spermine_synthase_animal UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SpmSyn_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:6611 UniProtKB/Swiss-Prot
NCBI Gene 6611 ENTREZGENE
OMIM 300105 OMIM
  309583 OMIM
PANTHER PTHR46315 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Spermine_synt_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SpmSyn_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA35972 PharmGKB
PROSITE PABS_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PABS_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53335 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt H7C2R7_HUMAN UniProtKB/TrEMBL
  P52788 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary A6NHA7 UniProtKB/Swiss-Prot
  A6NI34 UniProtKB/Swiss-Prot
  B2R9M0 UniProtKB/Swiss-Prot
  O00544 UniProtKB/Swiss-Prot
  Q9UQS1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-22 SMS  spermine synthase  SRS  Snyder-Robinson X-linked mental retardation syndrome  Data Merged 737654 PROVISIONAL
2012-05-08 SMS  spermine synthase  SMS  spermine synthase  Symbol and/or name change 5135510 APPROVED
2011-08-17 SMS  spermine synthase  SMS  spermine synthase  Symbol and/or name change 5135510 APPROVED