NLGN3 (neuroligin 3) - Rat Genome Database

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Gene: NLGN3 (neuroligin 3) Homo sapiens
Analyze
Symbol: NLGN3
Name: neuroligin 3
RGD ID: 733571
HGNC Page HGNC
Description: Exhibits scaffold protein binding activity. Involved in several processes, including learning; social behavior; and vocalization behavior. Localizes to cell surface and excitatory synapse. Implicated in Asperger syndrome and autistic disorder.
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: ASPGX1; AUTSX1; gliotactin homolog; HNL3; KIAA1480; neuroligin-3
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX71,144,831 - 71,171,201 (+)EnsemblGRCh38hg38GRCh38
GRCh38X71,144,389 - 71,175,307 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X70,364,691 - 70,391,051 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X70,281,436 - 70,307,776 (+)NCBINCBI36hg18NCBI36
Build 34X70,147,731 - 70,174,070NCBI
CeleraX70,718,556 - 70,744,930 (+)NCBI
Cytogenetic MapXq13.1NCBI
HuRefX64,183,444 - 64,209,758 (+)NCBIHuRef
CHM1_1X70,257,401 - 70,284,066 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adult behavior  (IMP)
axon extension  (ISS)
cell adhesion  (IEA)
chemical synaptic transmission  (IBA)
excitatory postsynaptic potential  (ISO)
inhibitory postsynaptic potential  (ISO,ISS)
learning  (IMP)
long-term synaptic potentiation  (ISO)
modulation of chemical synaptic transmission  (IBA,IEA,ISO,ISS)
negative regulation of dendritic spine morphogenesis  (ISO)
negative regulation of excitatory postsynaptic potential  (ISO)
neuron cell-cell adhesion  (IBA,ISS)
oligodendrocyte differentiation  (ISO)
positive regulation of AMPA receptor activity  (ISS)
positive regulation of dendritic spine development  (ISO)
positive regulation of excitatory postsynaptic potential  (ISS)
positive regulation of inhibitory postsynaptic potential  (ISO)
positive regulation of protein localization to synapse  (ISO)
positive regulation of synapse assembly  (ISS)
positive regulation of synaptic transmission, glutamatergic  (ISS)
positive regulation of synaptic vesicle clustering  (ISO)
postsynaptic membrane assembly  (IBA,ISS)
postsynaptic specialization assembly  (ISO)
presynapse assembly  (TAS)
presynaptic membrane assembly  (IBA,ISS)
receptor-mediated endocytosis  (ISS)
regulation of AMPA receptor activity  (ISO)
regulation of dendritic spine morphogenesis  (ISO)
regulation of long-term synaptic potentiation  (ISO)
regulation of NMDA receptor activity  (ISO)
regulation of respiratory gaseous exchange by nervous system process  (ISO,ISS)
regulation of synaptic transmission, glutamatergic  (ISO)
regulation of terminal button organization  (ISO)
rhythmic synaptic transmission  (ISS)
social behavior  (IMP,ISO)
synapse assembly  (ISS)
synapse organization  (IEA,IMP,ISO)
synaptic vesicle endocytosis  (IBA)
visual learning  (ISO)
vocalization behavior  (IMP)

Molecular Function

References

Additional References at PubMed
PMID:8576240   PMID:9278515   PMID:9325340   PMID:9751164   PMID:10767552   PMID:10819331   PMID:10996085   PMID:11329178   PMID:12477932   PMID:12669065   PMID:14702039   PMID:15150161  
PMID:15152050   PMID:15274046   PMID:15342556   PMID:15389766   PMID:15620359   PMID:15622415   PMID:16077734   PMID:16303743   PMID:16508939   PMID:16648374   PMID:17292328   PMID:18029348  
PMID:18189281   PMID:18628683   PMID:18976975   PMID:19058789   PMID:19406211   PMID:19645625   PMID:20034102   PMID:20227402   PMID:21569590   PMID:21838267   PMID:21873635   PMID:21988832  
PMID:22671294   PMID:23431752   PMID:23468870   PMID:23851596   PMID:24570023   PMID:24722188   PMID:25217961   PMID:25464930   PMID:25913192   PMID:26496610   PMID:26871637   PMID:27782075  
PMID:27805570   PMID:28514442   PMID:28611215   PMID:28948087   PMID:28959975   PMID:29503438   PMID:29622757   PMID:29792861   PMID:31119867   PMID:31150649   PMID:31184401  


Genomics

Comparative Map Data
NLGN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX71,144,831 - 71,171,201 (+)EnsemblGRCh38hg38GRCh38
GRCh38X71,144,389 - 71,175,307 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X70,364,691 - 70,391,051 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X70,281,436 - 70,307,776 (+)NCBINCBI36hg18NCBI36
Build 34X70,147,731 - 70,174,070NCBI
CeleraX70,718,556 - 70,744,930 (+)NCBI
Cytogenetic MapXq13.1NCBI
HuRefX64,183,444 - 64,209,758 (+)NCBIHuRef
CHM1_1X70,257,401 - 70,284,066 (+)NCBICHM1_1
Nlgn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X100,342,785 - 100,364,956 (+)NCBIGRCm39mm39
GRCm39 EnsemblX100,342,774 - 100,369,569 (+)Ensembl
GRCm38X101,299,179 - 101,321,350 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX101,299,168 - 101,325,963 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X98,494,520 - 98,516,689 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X97,501,929 - 97,524,067 (+)NCBImm8
CeleraX88,215,228 - 88,237,795 (+)NCBICelera
Cytogenetic MapXDNCBI
Nlgn3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X66,427,926 - 66,457,378 (+)NCBI
Rnor_6.0 EnsemblX71,199,491 - 71,222,732 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X71,199,390 - 71,227,460 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X72,051,846 - 72,075,119 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X89,376,193 - 89,398,665 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X89,449,625 - 89,471,949 (+)NCBI
CeleraX66,785,377 - 66,807,774 (+)NCBICelera
Cytogenetic MapXq22NCBI
Nlgn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547510,712,170 - 10,735,857 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495547510,712,170 - 10,735,857 (+)NCBIChiLan1.0ChiLan1.0
NLGN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X70,469,764 - 70,496,526 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX70,469,764 - 70,496,526 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X60,413,098 - 60,439,359 (+)NCBIMhudiblu_PPA_v0panPan3
NLGN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X55,510,729 - 55,532,396 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX55,513,626 - 55,531,371 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX46,337,800 - 46,359,510 (+)NCBI
ROS_Cfam_1.0X56,479,897 - 56,501,589 (+)NCBI
UMICH_Zoey_3.1X54,447,828 - 54,469,515 (+)NCBI
UNSW_CanFamBas_1.0X55,779,249 - 55,800,946 (+)NCBI
UU_Cfam_GSD_1.0X55,706,411 - 55,728,100 (+)NCBI
Nlgn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X46,672,077 - 46,696,110 (-)NCBI
SpeTri2.0NW_004936762435,729 - 458,261 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NLGN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX57,176,103 - 57,201,486 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X57,174,506 - 57,204,770 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X64,705,492 - 64,727,915 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NLGN3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X60,941,371 - 60,967,942 (+)NCBI
ChlSab1.1 EnsemblX60,941,654 - 60,967,936 (+)Ensembl
Nlgn3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249031,437,663 - 1,465,955 (+)NCBI

Position Markers
RH47725  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37X70,379,237 - 70,379,362UniSTSGRCh37
Build 36X70,295,962 - 70,296,087RGDNCBI36
CeleraX70,733,116 - 70,733,241RGD
Cytogenetic MapXq13.1UniSTS
HuRefX64,197,992 - 64,198,117UniSTS
GeneMap99-GB4 RH MapX238.28UniSTS
NCBI RH MapX374.5UniSTS
NLGN4X  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37X70,387,313 - 70,387,459UniSTSGRCh37
CeleraX70,741,192 - 70,741,338UniSTS
HuRefX64,206,010 - 64,206,156UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1865
Count of miRNA genes:724
Interacting mature miRNAs:846
Transcripts:ENST00000358741, ENST00000374051, ENST00000395855, ENST00000476589, ENST00000536169
Prediction methods: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
Medium 53 37 192 1 47 1 746 20 3175 11 265 3 2 1 576
Low 2284 2549 1129 254 1831 108 2800 1110 538 249 1135 1476 151 1146 1471 6 2
Below cutoff 99 403 390 357 69 344 806 1064 19 144 60 126 20 58 740

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_015874 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001166660 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001321276 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_018977 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_181303 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006724662 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006724663 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011530974 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017029597 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB040913 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF217411 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF217412 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF217413 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK074814 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK296217 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK299567 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK299669 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK314699 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL590764 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC028738 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC051715 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BP201014 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX641059 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471132 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  GQ489207 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KJ534889 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KJ534890 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KJ534891 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KJ534977 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KJ535034 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KJ535040 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KU178651 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KU178652 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000358741   ⟹   ENSP00000351591
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 EnsemblX71,144,841 - 71,171,201 (+)Ensembl
RefSeq Acc Id: ENST00000374051   ⟹   ENSP00000363163
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 EnsemblX71,144,843 - 71,171,201 (+)Ensembl
RefSeq Acc Id: ENST00000395855   ⟹   ENSP00000379196
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 EnsemblX71,144,843 - 71,167,757 (+)Ensembl
RefSeq Acc Id: ENST00000476589
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 EnsemblX71,153,456 - 71,171,199 (+)Ensembl
RefSeq Acc Id: ENST00000536169   ⟹   ENSP00000445298
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 EnsemblX71,144,831 - 71,171,199 (+)Ensembl
RefSeq Acc Id: ENST00000612180   ⟹   ENSP00000479877
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 EnsemblX71,144,836 - 71,171,114 (+)Ensembl
RefSeq Acc Id: NM_001166660   ⟹   NP_001160132
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X71,144,841 - 71,171,201 (+)NCBI
GRCh37X70,364,681 - 70,391,682 (+)NCBI
HuRefX64,183,444 - 64,209,758 (+)ENTREZGENE
CHM1_1X70,257,401 - 70,284,066 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001321276   ⟹   NP_001308205
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X71,144,841 - 71,171,201 (+)NCBI
CHM1_1X70,257,401 - 70,284,066 (+)NCBI
Sequence:
RefSeq Acc Id: NM_018977   ⟹   NP_061850
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X71,144,841 - 71,171,201 (+)NCBI
GRCh37X70,364,681 - 70,391,682 (+)NCBI
Build 36X70,281,436 - 70,307,776 (+)NCBI Archive
HuRefX64,183,444 - 64,209,758 (+)ENTREZGENE
CHM1_1X70,257,401 - 70,284,066 (+)NCBI
Sequence:
RefSeq Acc Id: NM_181303   ⟹   NP_851820
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X71,144,841 - 71,171,201 (+)NCBI
GRCh37X70,364,681 - 70,391,682 (+)NCBI
HuRefX64,183,444 - 64,209,758 (+)ENTREZGENE
CHM1_1X70,257,401 - 70,284,066 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006724662   ⟹   XP_006724725
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X71,146,160 - 71,170,537 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006724663   ⟹   XP_006724726
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X71,144,389 - 71,170,537 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011530974   ⟹   XP_011529276
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X71,144,389 - 71,170,537 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017029597   ⟹   XP_016885086
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X71,144,882 - 71,175,307 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001160132 (Get FASTA)   NCBI Sequence Viewer  
  NP_001308205 (Get FASTA)   NCBI Sequence Viewer  
  NP_061850 (Get FASTA)   NCBI Sequence Viewer  
  NP_851820 (Get FASTA)   NCBI Sequence Viewer  
  XP_006724725 (Get FASTA)   NCBI Sequence Viewer  
  XP_006724726 (Get FASTA)   NCBI Sequence Viewer  
  XP_011529276 (Get FASTA)   NCBI Sequence Viewer  
  XP_016885086 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF71230 (Get FASTA)   NCBI Sequence Viewer  
  AAF71231 (Get FASTA)   NCBI Sequence Viewer  
  AAF71232 (Get FASTA)   NCBI Sequence Viewer  
  AAF71233 (Get FASTA)   NCBI Sequence Viewer  
  AAH28738 (Get FASTA)   NCBI Sequence Viewer  
  AAH51715 (Get FASTA)   NCBI Sequence Viewer  
  ADB12634 (Get FASTA)   NCBI Sequence Viewer  
  AHW56529 (Get FASTA)   NCBI Sequence Viewer  
  AHW56530 (Get FASTA)   NCBI Sequence Viewer  
  AHW56531 (Get FASTA)   NCBI Sequence Viewer  
  AHW56617 (Get FASTA)   NCBI Sequence Viewer  
  AHW56673 (Get FASTA)   NCBI Sequence Viewer  
  AHW56679 (Get FASTA)   NCBI Sequence Viewer  
  ALQ34109 (Get FASTA)   NCBI Sequence Viewer  
  ALQ34110 (Get FASTA)   NCBI Sequence Viewer  
  BAA96004 (Get FASTA)   NCBI Sequence Viewer  
  BAC11226 (Get FASTA)   NCBI Sequence Viewer  
  BAG37248 (Get FASTA)   NCBI Sequence Viewer  
  BAH12284 (Get FASTA)   NCBI Sequence Viewer  
  BAH13067 (Get FASTA)   NCBI Sequence Viewer  
  BAH13096 (Get FASTA)   NCBI Sequence Viewer  
  CAE46030 (Get FASTA)   NCBI Sequence Viewer  
  EAX05307 (Get FASTA)   NCBI Sequence Viewer  
  EAX05308 (Get FASTA)   NCBI Sequence Viewer  
  EAX05309 (Get FASTA)   NCBI Sequence Viewer  
  EAX05310 (Get FASTA)   NCBI Sequence Viewer  
  EAX05311 (Get FASTA)   NCBI Sequence Viewer  
  EAX05312 (Get FASTA)   NCBI Sequence Viewer  
  EAX05313 (Get FASTA)   NCBI Sequence Viewer  
  Q9NZ94 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_851820   ⟸   NM_181303
- Peptide Label: isoform 1 precursor
- UniProtKB: Q9NZ94 (UniProtKB/Swiss-Prot),   X5DNV3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_061850   ⟸   NM_018977
- Peptide Label: isoform 2 precursor
- UniProtKB: Q9NZ94 (UniProtKB/Swiss-Prot),   Q4G160 (UniProtKB/TrEMBL),   X5D2P6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001160132   ⟸   NM_001166660
- Peptide Label: isoform 3 precursor
- UniProtKB: Q9NZ94 (UniProtKB/Swiss-Prot),   Q4G160 (UniProtKB/TrEMBL),   X5D7L6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006724726   ⟸   XM_006724663
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006724725   ⟸   XM_006724662
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_011529276   ⟸   XM_011530974
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: NP_001308205   ⟸   NM_001321276
- Peptide Label: isoform 4
- UniProtKB: Q9NZ94 (UniProtKB/Swiss-Prot),   B7Z3P8 (UniProtKB/TrEMBL),   Q6MZK0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_016885086   ⟸   XM_017029597
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSP00000363163   ⟸   ENST00000374051
RefSeq Acc Id: ENSP00000479877   ⟸   ENST00000612180
RefSeq Acc Id: ENSP00000445298   ⟸   ENST00000536169
RefSeq Acc Id: ENSP00000379196   ⟸   ENST00000395855
RefSeq Acc Id: ENSP00000351591   ⟸   ENST00000358741
Protein Domains
COesterase

Promoters
RGD ID:6809078
Promoter ID:HG_KWN:67166
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:NM_001166660,   NM_181303,   OTTHUMT00000057120,   UC004DZC.1,   UC010NLB.1
Position:
Human AssemblyChrPosition (strand)Source
Build 36X70,280,541 - 70,281,542 (+)MPROMDB
RGD ID:6809079
Promoter ID:HG_KWN:67167
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:UC004DZD.1
Position:
Human AssemblyChrPosition (strand)Source
Build 36X70,283,131 - 70,284,597 (+)MPROMDB
RGD ID:13627404
Promoter ID:EPDNEW_H28976
Type:initiation region
Name:NLGN3_1
Description:neuroligin 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H28977  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X71,144,843 - 71,144,903EPDNEW
RGD ID:13627402
Promoter ID:EPDNEW_H28977
Type:multiple initiation site
Name:NLGN3_2
Description:neuroligin 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H28976  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38X71,153,413 - 71,153,473EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
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
NM_181303.2(NLGN3):c.1583C>G (p.Pro528Arg) single nucleotide variant not provided [RCV000520257] ChrX:71167680 [GRCh38]
ChrX:70387530 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.1411C>T (p.Arg471Cys) single nucleotide variant Asperger syndrome X-linked 1 [RCV000012080]|Autism, susceptibility to, X-linked 1 [RCV000032611] ChrX:71167508 [GRCh38]
ChrX:70387358 [GRCh37]
ChrX:Xq13.1
risk factor
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:10679-156013167)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-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 Xp11.21-q28(chrX:57372584-155996431)x1 copy number loss See cases [RCV000051665] ChrX:57372584..155996431 [GRCh38]
ChrX:57399017..155226096 [GRCh37]
ChrX:57415742..154879290 [NCBI36]
ChrX:Xp11.21-q28
pathogenic
GRCh38/hg38 Xq11.1-28(chrX:63279794-155939524)x1 copy number loss See cases [RCV000051666] ChrX:63279794..155939524 [GRCh38]
ChrX:62499671..155169188 [GRCh37]
ChrX:62416396..154822382 [NCBI36]
ChrX:Xq11.1-28
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 Xq12-21.1(chrX:67621041-76868590)x2 copy number gain See cases [RCV000052416] ChrX:67621041..76868590 [GRCh38]
ChrX:66840883..76009501 [GRCh37]
ChrX:66757608..76005403 [NCBI36]
ChrX:Xq12-21.1
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 Xq12-13.3(chrX:68382004-75243150)x2 copy number gain See cases [RCV000052417] ChrX:68382004..75243150 [GRCh38]
ChrX:67601846..74462985 [GRCh37]
ChrX:67518571..74379710 [NCBI36]
ChrX:Xq12-13.3
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: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-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-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
NM_181303.2(NLGN3):c.2250C>T (p.Ala750=) single nucleotide variant History of neurodevelopmental disorder [RCV000715722]|not provided [RCV000973058]|not specified [RCV000081974] ChrX:71169800 [GRCh38]
ChrX:70389650 [GRCh37]
ChrX:Xq13.1
benign
NM_181303.2(NLGN3):c.282G>A (p.Ser94=) single nucleotide variant History of neurodevelopmental disorder [RCV000720974]|not provided [RCV000081975] ChrX:71148031 [GRCh38]
ChrX:70367881 [GRCh37]
ChrX:Xq13.1
likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_181303.2(NLGN3):c.594T>C (p.Gly198=) single nucleotide variant History of neurodevelopmental disorder [RCV000716715]|not specified [RCV000081976] ChrX:71155230 [GRCh38]
ChrX:70375080 [GRCh37]
ChrX:Xq13.1
benign|likely benign|conflicting interpretations of pathogenicity|uncertain significance
NM_181303.2(NLGN3):c.603C>T (p.Pro201=) single nucleotide variant not provided [RCV000081977] ChrX:71155239 [GRCh38]
ChrX:70375089 [GRCh37]
ChrX:Xq13.1
uncertain significance
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
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-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: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-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: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: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 Xq11.1-21.1(chrX:62712219-78605009)x3 copy number gain See cases [RCV000134569] ChrX:62712219..78605009 [GRCh38]
ChrX:61931689..77860506 [GRCh37]
ChrX:61848414..77747162 [NCBI36]
ChrX:Xq11.1-21.1
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 Xq11.1-28(chrX:62712230-155978888)x3 copy number gain See cases [RCV000134025] ChrX:62712230..155978888 [GRCh38]
ChrX:61931700..155208553 [GRCh37]
ChrX:61848425..154861747 [NCBI36]
ChrX:Xq11.1-28
pathogenic
GRCh38/hg38 Xp21.1-q28(chrX:37076284-156016920)x1 copy number loss See cases [RCV000135300] ChrX:37076284..156016920 [GRCh38]
ChrX:37094357..155246585 [GRCh37]
ChrX:37004278..154899779 [NCBI36]
ChrX:Xp21.1-q28
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 Xp11.22-q21.31(chrX:53985575-92203108)x1 copy number loss See cases [RCV000135306] ChrX:53985575..92203108 [GRCh38]
ChrX:54012008..91458107 [GRCh37]
ChrX:54028733..91344763 [NCBI36]
ChrX:Xp11.22-q21.31
pathogenic
GRCh38/hg38 Xp21.1-q28(chrX:36237706-156022206)x1 copy number loss See cases [RCV000135552] ChrX:36237706..156022206 [GRCh38]
ChrX:36255823..155251871 [GRCh37]
ChrX:36165744..154905065 [NCBI36]
ChrX:Xp21.1-q28
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 Xq13.1(chrX:70974174-71207055)x2 copy number gain See cases [RCV000136018] ChrX:70974174..71207055 [GRCh38]
ChrX:70194024..70426905 [GRCh37]
ChrX:70110749..70343630 [NCBI36]
ChrX:Xq13.1
uncertain significance
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-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-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 Xq11.1-28(chrX:62561604-156003242)x3 copy number gain See cases [RCV000137553] ChrX:62561604..156003242 [GRCh38]
ChrX:61781074..155232907 [GRCh37]
ChrX:61697799..154886101 [NCBI36]
ChrX:Xq11.1-28
pathogenic
GRCh38/hg38 Xp11.23-q22.1(chrX:49100536-102174742)x1 copy number loss See cases [RCV000137414] ChrX:49100536..102174742 [GRCh38]
ChrX:48957474..101429714 [GRCh37]
ChrX:48844418..101316370 [NCBI36]
ChrX:Xp11.23-q22.1
pathogenic|likely benign
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-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-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 Xq11.1-28(chrX:62712219-156003242)x3 copy number gain See cases [RCV000139416] ChrX:62712219..156003242 [GRCh38]
ChrX:61931689..155232907 [GRCh37]
ChrX:61848414..154886101 [NCBI36]
ChrX:Xq11.1-28
pathogenic|likely benign
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-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-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 Xp11.22-q24(chrX:50289384-119297604) copy number loss See cases [RCV000141742] ChrX:50289384..119297604 [GRCh38]
ChrX:50032384..118431567 [GRCh37]
ChrX:50049124..118315595 [NCBI36]
ChrX:Xp11.22-q24
pathogenic
GRCh38/hg38 Xq12-21.1(chrX:66445907-78172208)x3 copy number gain See cases [RCV000142336] ChrX:66445907..78172208 [GRCh38]
ChrX:65665749..77427705 [GRCh37]
ChrX:65582474..77314361 [NCBI36]
ChrX:Xq12-21.1
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 Xp11.22-q28(chrX:53144751-156003242)x1 copy number loss See cases [RCV000143349] ChrX:53144751..156003242 [GRCh38]
ChrX:53321095..155232907 [GRCh37]
ChrX:53190658..154886101 [NCBI36]
ChrX:Xp11.22-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-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 Xp11.21-q13.3(chrX:56431359-76557419)x1 copy number loss See cases [RCV000143131] ChrX:56431359..76557419 [GRCh38]
ChrX:56457792..75777827 [GRCh37]
ChrX:56474517..75694231 [NCBI36]
ChrX:Xp11.21-q13.3
pathogenic
GRCh38/hg38 Xq13.1(chrX:71071787-71777197)x2 copy number gain See cases [RCV000143302] ChrX:71071787..71777197 [GRCh38]
ChrX:70291637..70997047 [GRCh37]
ChrX:70208362..70913772 [NCBI36]
ChrX:Xq13.1
uncertain significance
GRCh38/hg38 Xq13.1(chrX:71022322-71682982)x2 copy number gain See cases [RCV000143525] ChrX:71022322..71682982 [GRCh38]
ChrX:70242172..70902832 [GRCh37]
ChrX:70158897..70819557 [NCBI36]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.1954A>G (p.Thr652Ala) single nucleotide variant History of neurodevelopmental disorder [RCV000716834]|not provided [RCV000488237]|not specified [RCV000153575] ChrX:71169504 [GRCh38]
ChrX:70389354 [GRCh37]
ChrX:Xq13.1
benign|likely benign
NM_181303.2(NLGN3):c.2034C>T (p.Tyr678=) single nucleotide variant History of neurodevelopmental disorder [RCV000715642]|not provided [RCV000891351]|not specified [RCV000153577] ChrX:71169584 [GRCh38]
ChrX:70389434 [GRCh37]
ChrX:Xq13.1
benign|likely benign
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_181303.2(NLGN3):c.2011C>T (p.Arg671Trp) single nucleotide variant not provided [RCV000153576] ChrX:71169561 [GRCh38]
ChrX:70389411 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.20C>T (p.Pro7Leu) single nucleotide variant not provided [RCV000175914] ChrX:71147769 [GRCh38]
ChrX:70367619 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.435C>T (p.Asn145=) single nucleotide variant not specified [RCV000192631] ChrX:71148184 [GRCh38]
ChrX:70368034 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.1703+5G>T single nucleotide variant not specified [RCV000193209] ChrX:71167805 [GRCh38]
ChrX:70387655 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.583C>T (p.Arg195Trp) single nucleotide variant not provided [RCV000178320] ChrX:71155219 [GRCh38]
ChrX:70375069 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.2331C>T (p.Ala777=) single nucleotide variant not specified [RCV000194418] ChrX:71169881 [GRCh38]
ChrX:70389731 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.1473C>T (p.Ala491=) single nucleotide variant not specified [RCV000194986] ChrX:71167570 [GRCh38]
ChrX:70387420 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.839G>A (p.Arg280His) single nucleotide variant not provided [RCV000178973] ChrX:71164254 [GRCh38]
ChrX:70384104 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.1176G>A (p.Glu392=) single nucleotide variant not provided [RCV000179506] ChrX:71167273 [GRCh38]
ChrX:70387123 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.*8T>C single nucleotide variant not provided [RCV000179960] ChrX:71170105 [GRCh38]
ChrX:70389955 [GRCh37]
ChrX:Xq13.1
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 Xq11.1-28(chrX:62063537-155246643)x3 copy number gain See cases [RCV000240143] ChrX:62063537..155246643 [GRCh37]
ChrX:Xq11.1-28
pathogenic
NM_181303.2(NLGN3):c.652A>C (p.Met218Leu) single nucleotide variant not specified [RCV000193504] ChrX:71155288 [GRCh38]
ChrX:70375138 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.981A>G (p.Pro327=) single nucleotide variant not specified [RCV000194364] ChrX:71167078 [GRCh38]
ChrX:70386928 [GRCh37]
ChrX:Xq13.1
uncertain significance
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 Xp22.33-q28(chrX:71267-155255839)x1 copy number loss See cases [RCV000239832] ChrX:71267..155255839 [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
NM_181303.2(NLGN3):c.1849C>T (p.Arg617Trp) single nucleotide variant Intellectual disability [RCV000224769] ChrX:71169399 [GRCh38]
ChrX:70389249 [GRCh37]
ChrX:Xq13.1
likely pathogenic
GRCh37/hg19 Xp11.21-q21.1(chrX:55240087-78225374)x1 copy number loss See cases [RCV000511311] ChrX:55240087..78225374 [GRCh37]
ChrX:Xp11.21-q21.1
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:553069-155233731)x1 copy number loss See cases [RCV000446026] ChrX:553069..155233731 [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 Xp11.3-q21.1(chrX:44734936-79676121)x3 copy number gain See cases [RCV000240019] ChrX:44734936..79676121 [GRCh37]
ChrX:Xp11.3-q21.1
pathogenic
GRCh37/hg19 Xp11.21-q28(chrX:56457791-155233731)x3 copy number gain See cases [RCV000511307] ChrX:56457791..155233731 [GRCh37]
ChrX:Xp11.21-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 Xq11.1-28(chrX:62063537-155250222)x3 copy number gain See cases [RCV000240148] ChrX:62063537..155250222 [GRCh37]
ChrX:Xq11.1-28
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
NM_181303.2(NLGN3):c.603C>G (p.Pro201=) single nucleotide variant History of neurodevelopmental disorder [RCV000719268]|not provided [RCV000378007] ChrX:71155239 [GRCh38]
ChrX:70375089 [GRCh37]
ChrX:Xq13.1
likely benign|uncertain significance
NM_181303.2(NLGN3):c.10C>T (p.Arg4Trp) single nucleotide variant History of neurodevelopmental disorder [RCV000721072]|not provided [RCV000487940] ChrX:71147759 [GRCh38]
ChrX:70367609 [GRCh37]
ChrX:Xq13.1
benign|conflicting interpretations of pathogenicity|uncertain significance
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
Single allele duplication Syndromic X-linked intellectual disability Lubs type [RCV000768455] ChrX:15323210..153542100 [GRCh37]
ChrX:Xp22.2-q28
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-q28(chrX:70297-155255792) copy number loss See cases [RCV000449461] ChrX:70297..155255792 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xq13.1-28(chrX:68701338-155233731)x3 copy number gain See cases [RCV000446471] ChrX:68701338..155233731 [GRCh37]
ChrX:Xq13.1-28
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: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:318707-155224707)x1 copy number loss See cases [RCV000446667] ChrX:318707..155224707 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp11.1-q28(chrX:58140271-155046703)x3 copy number gain See cases [RCV000446151] ChrX:58140271..155046703 [GRCh37]
ChrX:Xp11.1-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
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-q28(chrX:70297-155246585)x1 copy number loss See cases [RCV000448652] ChrX:70297..155246585 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp11.21-q28(chrX:55532799-150239235)x1 copy number loss See cases [RCV000448870] ChrX:55532799..150239235 [GRCh37]
ChrX:Xp11.21-q28
pathogenic
NM_181303.2(NLGN3):c.21G>A (p.Pro7=) single nucleotide variant not specified [RCV000504378] ChrX:71147770 [GRCh38]
ChrX:70367620 [GRCh37]
ChrX:Xq13.1
likely benign|uncertain significance
GRCh37/hg19 Xp22.33-q28(chrX:168547-151304063)x1 copy number loss See cases [RCV000510382] ChrX:168547..151304063 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
NM_181303.2(NLGN3):c.2243G>A (p.Arg748Gln) single nucleotide variant not specified [RCV000504410] ChrX:71169793 [GRCh38]
ChrX:70389643 [GRCh37]
ChrX:Xq13.1
uncertain significance
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 Xp11.21-q28(chrX:55000501-155230750)x3 copy number gain See cases [RCV000511787] ChrX:55000501..155230750 [GRCh37]
ChrX:Xp11.21-q28
pathogenic
GRCh37/hg19 Xp21.1-q22.1(chrX:37521774-98488534)x1 copy number loss See cases [RCV000512026] ChrX:37521774..98488534 [GRCh37]
ChrX:Xp21.1-q22.1
pathogenic
GRCh37/hg19 Xp21.2-q28(chrX:31088082-155233731)x1 copy number loss See cases [RCV000511413] ChrX:31088082..155233731 [GRCh37]
ChrX:Xp21.2-q28
pathogenic
GRCh37/hg19 Xq13.1(chrX:70287671-70997047)x3 copy number gain See cases [RCV000511625] ChrX:70287671..70997047 [GRCh37]
ChrX:Xq13.1
uncertain significance
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 Xp11.21-q28(chrX:57511767-155233731)x3 copy number gain See cases [RCV000510826] ChrX:57511767..155233731 [GRCh37]
ChrX:Xp11.21-q28
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 Xq13.1(chrX:70287671-70997047)x2 copy number gain See cases [RCV000512522] ChrX:70287671..70997047 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.2353C>T (p.Arg785Cys) single nucleotide variant not provided [RCV000514171] ChrX:71169903 [GRCh38]
ChrX:70389753 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.214dup (p.Val72fs) duplication Inborn genetic diseases [RCV000622474] ChrX:71147958..71147959 [GRCh38]
ChrX:70367808..70367809 [GRCh37]
ChrX:Xq13.1
pathogenic
GRCh37/hg19 Xp11.21-q28(chrX:57415659-155233731)x3 copy number gain See cases [RCV000512173] ChrX:57415659..155233731 [GRCh37]
ChrX:Xp11.21-q28
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
NM_181303.2(NLGN3):c.-5G>A single nucleotide variant History of neurodevelopmental disorder [RCV000716384] ChrX:71147745 [GRCh38]
ChrX:70367595 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.2220C>T (p.Pro740=) single nucleotide variant History of neurodevelopmental disorder [RCV000716107] ChrX:71169770 [GRCh38]
ChrX:70389620 [GRCh37]
ChrX:Xq13.1
likely benign
NM_181303.2(NLGN3):c.642G>C (p.Gly214=) single nucleotide variant History of neurodevelopmental disorder [RCV000718558] ChrX:71155278 [GRCh38]
ChrX:70375128 [GRCh37]
ChrX:Xq13.1
likely benign
NM_181303.2(NLGN3):c.51G>A (p.Thr17=) single nucleotide variant History of neurodevelopmental disorder [RCV000718848] ChrX:71147800 [GRCh38]
ChrX:70367650 [GRCh37]
ChrX:Xq13.1
likely benign
NM_181303.2(NLGN3):c.1976C>A (p.Thr659Asn) single nucleotide variant History of neurodevelopmental disorder [RCV000719925] ChrX:71169526 [GRCh38]
ChrX:70389376 [GRCh37]
ChrX:Xq13.1
uncertain significance
GRCh37/hg19 Xp11.23-q13.2(chrX:48115450-73424191)x1 copy number loss not provided [RCV000753535] ChrX:48115450..73424191 [GRCh37]
ChrX:Xp11.23-q13.2
pathogenic
GRCh37/hg19 Xq13.1(chrX:70313664-70568458)x2 copy number gain not provided [RCV000753588] ChrX:70313664..70568458 [GRCh37]
ChrX:Xq13.1
benign
GRCh37/hg19 Xq13.1(chrX:70323237-70431963)x2 copy number gain not provided [RCV000753589] ChrX:70323237..70431963 [GRCh37]
ChrX:Xq13.1
benign
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)x1 copy number loss not provided [RCV000753271] ChrX:60262..155245765 [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
Single allele duplication Autistic disorder of childhood onset [RCV000754365] ChrX:1..156040895 [GRCh38]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xq11.1-28(chrX:61694576-155254881)x1 copy number loss not provided [RCV000753556] ChrX:61694576..155254881 [GRCh37]
ChrX:Xq11.1-28
pathogenic
NC_000023.10:g.36649710_136649711del100000002insG indel Heterotaxy, visceral, 1, X-linked [RCV000754886] ChrX:36649710..136649711 [GRCh37]
ChrX:Xp21.1-q26.3
pathogenic
NM_181303.2(NLGN3):c.1818C>T (p.Ile606=) single nucleotide variant not provided [RCV000902476] ChrX:71169368 [GRCh38]
ChrX:70389218 [GRCh37]
ChrX:Xq13.1
likely benign
NM_181303.2(NLGN3):c.2370C>T (p.Pro790=) single nucleotide variant not provided [RCV000899295] ChrX:71169920 [GRCh38]
ChrX:70389770 [GRCh37]
ChrX:Xq13.1
benign
NM_181303.2(NLGN3):c.577+9G>A single nucleotide variant not provided [RCV000923622] ChrX:71153545 [GRCh38]
ChrX:70373395 [GRCh37]
ChrX:Xq13.1
likely benign
NM_181303.2(NLGN3):c.796C>T (p.Arg266Cys) single nucleotide variant not provided [RCV000995946] ChrX:71164211 [GRCh38]
ChrX:70384061 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.1716G>A (p.Lys572=) single nucleotide variant not provided [RCV000995947] ChrX:71169266 [GRCh38]
ChrX:70389116 [GRCh37]
ChrX:Xq13.1
uncertain significance
46,Y,inv(X)(p21.1q13.3) inversion Elevated serum creatine phosphokinase [RCV000856573] ChrX:32196272..75245806 [GRCh37]
ChrX:Xp21.1-q13.3
likely pathogenic
NM_181303.2(NLGN3):c.1600C>T (p.Pro534Ser) single nucleotide variant Autistic behavior [RCV000778067] ChrX:71167697 [GRCh38]
ChrX:70387547 [GRCh37]
ChrX:Xq13.1
pathogenic
NM_181303.2(NLGN3):c.807C>T (p.Ser269=) single nucleotide variant not provided [RCV000896190] ChrX:71164222 [GRCh38]
ChrX:70384072 [GRCh37]
ChrX:Xq13.1
benign
NM_181303.2(NLGN3):c.2142G>A (p.Val714=) single nucleotide variant not provided [RCV000841514] ChrX:71169692 [GRCh38]
ChrX:70389542 [GRCh37]
ChrX:Xq13.1
likely benign
NM_181303.2(NLGN3):c.26C>T (p.Ser9Leu) single nucleotide variant not specified [RCV001193947] ChrX:71147775 [GRCh38]
ChrX:70367625 [GRCh37]
ChrX:Xq13.1
uncertain significance
GRCh37/hg19 Xp11.21-q28(chrX:54941868-155233731)x1 copy number loss not provided [RCV000848218] ChrX:54941868..155233731 [GRCh37]
ChrX:Xp11.21-q28
uncertain significance
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 Xp11.4-q21.32(chrX:40572613-92796528)x1 copy number loss not provided [RCV000845670] ChrX:40572613..92796528 [GRCh37]
ChrX:Xp11.4-q21.32
pathogenic
GRCh37/hg19 Xp22.33-q28(chrX:168546-155233731)x4 copy number gain not provided [RCV000846039] ChrX:168546..155233731 [GRCh37]
ChrX:Xp22.33-q28
pathogenic
GRCh37/hg19 Xp11.1-q28(chrX:58455352-155233731)x1 copy number loss not provided [RCV000846274] ChrX:58455352..155233731 [GRCh37]
ChrX:Xp11.1-q28
pathogenic
NM_181303.2(NLGN3):c.728-4_728-3dup duplication not provided [RCV000890722] ChrX:71164138..71164139 [GRCh38]
ChrX:70383988..70383989 [GRCh37]
ChrX:Xq13.1
likely benign
NC_000023.11:g.(?_71118745)_(71224569_?)dup duplication FG syndrome 1 [RCV001033220] ChrX:70338595..70444419 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.38G>A (p.Ser13Asn) single nucleotide variant not specified [RCV001175512] ChrX:71147787 [GRCh38]
ChrX:70367637 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.913+11C>G single nucleotide variant Autism, susceptibility to, X-linked 1 [RCV001197755] ChrX:71164339 [GRCh38]
ChrX:70384189 [GRCh37]
ChrX:Xq13.1
benign
NM_181303.2(NLGN3):c.244A>C (p.Lys82Gln) single nucleotide variant Intellectual disability [RCV001251852] ChrX:71147993 [GRCh38]
ChrX:70367843 [GRCh37]
ChrX:Xq13.1
likely benign
NM_181303.2(NLGN3):c.2435C>G (p.Thr812Ser) single nucleotide variant Inborn genetic diseases [RCV001266464] ChrX:71169985 [GRCh38]
ChrX:70389835 [GRCh37]
ChrX:Xq13.1
uncertain significance
GRCh37/hg19 Xp11.21-q28(chrX:55507789-155198481)x3 copy number gain See cases [RCV001263024] ChrX:55507789..155198481 [GRCh37]
ChrX:Xp11.21-q28
pathogenic
NM_181303.2(NLGN3):c.163C>G (p.Arg55Gly) single nucleotide variant Intellectual disability [RCV001257609] ChrX:71147912 [GRCh38]
ChrX:70367762 [GRCh37]
ChrX:Xq13.1
uncertain significance
GRCh37/hg19 Xq13.1(chrX:70386654-70743623)x0 copy number gain See cases [RCV001263049] ChrX:70386654..70743623 [GRCh37]
ChrX:Xq13.1
uncertain significance
NM_181303.2(NLGN3):c.2161C>T (p.Leu721Phe) single nucleotide variant Complex neurodevelopmental disorder [RCV001270905] ChrX:71169711 [GRCh38]
ChrX:70389561 [GRCh37]
ChrX:Xq13.1
uncertain significance
GRCh37/hg19 Xp11.21-q28(chrX:56469080-155233731)x3 copy number gain not provided [RCV001281359] ChrX:56469080..155233731 [GRCh37]
ChrX:Xp11.21-q28
pathogenic
NM_181303.2(NLGN3):c.707A>G (p.Asn236Ser) single nucleotide variant Autism, susceptibility to, X-linked 1 [RCV001329099] ChrX:71155343 [GRCh38]
ChrX:70375193 [GRCh37]
ChrX:Xq13.1
uncertain significance

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:14289 AgrOrtholog
COSMIC NLGN3 COSMIC
Ensembl Genes ENSG00000196338 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000351591 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000363163 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000379196 UniProtKB/TrEMBL
  ENSP00000445298 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000479877 UniProtKB/TrEMBL
Ensembl Transcript ENST00000358741 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000374051 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000395855 UniProtKB/TrEMBL
  ENST00000476589 ENTREZGENE
  ENST00000536169 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000612180 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.1820 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000196338 GTEx
HGNC ID HGNC:14289 ENTREZGENE
Human Proteome Map NLGN3 Human Proteome Map
InterPro AB_hydrolase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CarbesteraseB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Carboxylesterase_B_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nlgn UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NLGN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:54413 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 54413 ENTREZGENE
OMIM 300336 OMIM
  300425 OMIM
  300494 OMIM
PANTHER PTHR43903:SF4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam COesterase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA31649 PharmGKB
PRINTS NEUROLIGIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CARBOXYLESTERASE_B_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53474 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A087WW27_HUMAN UniProtKB/TrEMBL
  A0A0S2Z5K2_HUMAN UniProtKB/TrEMBL
  B7Z3P8 ENTREZGENE, UniProtKB/TrEMBL
  E7EVK0_HUMAN UniProtKB/TrEMBL
  NLGN3_HUMAN UniProtKB/Swiss-Prot
  Q4G160 ENTREZGENE, UniProtKB/TrEMBL
  Q6MZK0 ENTREZGENE, UniProtKB/TrEMBL
  Q9NZ94 ENTREZGENE
  X5D2P6 ENTREZGENE, UniProtKB/TrEMBL
  X5D307_HUMAN UniProtKB/TrEMBL
  X5D7L6 ENTREZGENE, UniProtKB/TrEMBL
  X5D9J9_HUMAN UniProtKB/TrEMBL
  X5DNV3 ENTREZGENE, UniProtKB/TrEMBL
  X5DRC3_HUMAN UniProtKB/TrEMBL
UniProt Secondary B2RBK1 UniProtKB/Swiss-Prot
  D2X2H6 UniProtKB/Swiss-Prot
  D3DVV0 UniProtKB/Swiss-Prot
  D3DVV1 UniProtKB/Swiss-Prot
  Q86V51 UniProtKB/Swiss-Prot
  Q8NCD0 UniProtKB/Swiss-Prot
  Q9NZ95 UniProtKB/Swiss-Prot
  Q9NZ96 UniProtKB/Swiss-Prot
  Q9NZ97 UniProtKB/Swiss-Prot
  Q9P248 UniProtKB/Swiss-Prot