MSX2 (msh homeobox 2) - Rat Genome Database

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Gene: MSX2 (msh homeobox 2) Homo sapiens
Analyze
Symbol: MSX2
Name: msh homeobox 2
RGD ID: 735997
HGNC Page HGNC
Description: Enables sequence-specific double-stranded DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in cytosol and nuclear speck. Implicated in craniosynostosis and parietal foramina.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: CRS2; FPP; homeobox protein Hox-8; homeobox protein MSX-2; HOX8; MSH; msh homeo box 2; msh homeo box homolog 2 (drosophila); msh homeobox homolog 2; PFM; PFM1
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: MSX2P1  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385174,724,582 - 174,730,896 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl5174,724,582 - 174,730,896 (+)EnsemblGRCh38hg38GRCh38
GRCh375174,151,585 - 174,157,899 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365174,084,181 - 174,090,508 (+)NCBINCBI36hg18NCBI36
Build 345174,084,207 - 174,090,507NCBI
Celera5170,185,579 - 170,191,910 (+)NCBI
Cytogenetic Map5q35.2NCBI
HuRef5169,246,978 - 169,253,303 (+)NCBIHuRef
CHM1_15173,583,988 - 173,590,298 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,6-dinitrotoluene  (ISO)
2-ethylhexan-1-ol  (ISO)
3,7-dihydropurine-6-thione  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-fluorouracil  (EXP)
acrylamide  (ISO)
aflatoxin B1  (EXP)
all-trans-retinoic acid  (EXP,ISO)
ammonium chloride  (ISO)
arsenite(3-)  (EXP)
arsenous acid  (EXP)
belinostat  (EXP)
benzalkonium chloride  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[e]pyrene  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
cadmium dichloride  (ISO)
cadmium sulfate  (ISO)
calcitriol  (EXP)
carbamazepine  (EXP)
carbon nanotube  (ISO)
cobalt dichloride  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
coumestrol  (EXP)
Cuprizon  (ISO)
deoxynivalenol  (EXP)
dexamethasone  (ISO)
diarsenic trioxide  (EXP)
diethylstilbestrol  (ISO)
dioxygen  (EXP)
dorsomorphin  (EXP)
doxorubicin  (EXP)
entinostat  (EXP)
folic acid  (ISO)
furan  (ISO)
genistein  (ISO)
glycerol 2-phosphate  (ISO)
hexaconazole  (ISO)
L-ascorbic acid  (ISO)
lead diacetate  (ISO)
lipopolysaccharide  (ISO)
manganese(II) chloride  (ISO)
mercaptopurine  (ISO)
mercury dibromide  (EXP)
methapyrilene  (EXP)
methylmercury chloride  (EXP)
Muraglitazar  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (ISO)
p-chloromercuribenzoic acid  (EXP)
panobinostat  (EXP)
phenethyl caffeate  (ISO)
phenylmercury acetate  (EXP)
potassium phosphate  (ISO)
progesterone  (ISO)
purine-6-thiol  (ISO)
retinyl acetate  (ISO)
SB 431542  (EXP)
silicon dioxide  (EXP)
sunitinib  (EXP)
tebuconazole  (EXP)
Tesaglitazar  (ISO)
triadimefon  (ISO)
trichostatin A  (EXP)
troglitazone  (ISO)
valproic acid  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of meiosis  (IEA,ISO)
anterior/posterior pattern specification  (IEA,ISO)
BMP signaling pathway  (IEA,ISO)
BMP signaling pathway involved in heart development  (IEA,ISO)
bone morphogenesis  (IEA,ISO)
bone trabecula formation  (IEA,ISO)
branching involved in mammary gland duct morphogenesis  (IEA,ISO)
cardiac conduction system development  (NAS)
cartilage development  (IEA,ISO)
cellular response to estradiol stimulus  (IEA,ISO)
cellular response to growth factor stimulus  (IEA,ISO)
chondrocyte development  (IEA,ISO)
cranial suture morphogenesis  (TAS)
embryonic digit morphogenesis  (IEA,ISO)
embryonic forelimb morphogenesis  (IEA,ISO)
embryonic hindlimb morphogenesis  (IEA,ISO)
embryonic limb morphogenesis  (IEA,ISO)
embryonic morphogenesis  (IBA)
embryonic nail plate morphogenesis  (IEA,ISO)
enamel mineralization  (IEA,ISO)
endochondral bone growth  (IEA,ISO)
epithelial to mesenchymal transition involved in endocardial cushion formation  (IEA,ISO)
frontal suture morphogenesis  (IEA,ISO)
mammary gland epithelium development  (IEA,ISO)
mesenchymal cell apoptotic process  (IEA,ISO)
negative regulation of apoptotic process  (IEA,ISO)
negative regulation of cell population proliferation  (IEA,ISO)
negative regulation of CREB transcription factor activity  (IEA,ISO)
negative regulation of fat cell differentiation  (IEA,ISO)
negative regulation of keratinocyte differentiation  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IEA,IMP,ISO,ISS)
negative regulation of transcription regulatory region DNA binding  (IEA,ISO,ISS)
negative regulation of transcription, DNA-templated  (IEA,ISS)
odontogenesis  (IEA,ISO)
ossification  (IEA,ISO)
osteoblast development  (IEA,ISO)
osteoblast differentiation  (IEA,ISS)
outflow tract morphogenesis  (IEA,ISO)
outflow tract septum morphogenesis  (IEA,ISO)
positive regulation of apoptotic process  (ISO)
positive regulation of BMP signaling pathway  (IEA,ISO)
positive regulation of cell death  (ISO)
positive regulation of mesenchymal cell apoptotic process  (IEA,ISO)
positive regulation of osteoblast differentiation  (IEA,ISO)
positive regulation of timing of catagen  (IEA,ISO)
regulation of apoptotic process  (IEA,ISO)
regulation of transcription by RNA polymerase II  (IBA)
regulation of transcription, DNA-templated  (IEA)
signal transduction involved in regulation of gene expression  (IEA,ISO)
stem cell differentiation  (IEA,ISO)
transcription by RNA polymerase II  (ISO)
wound healing  (IEA,ISO)
wound healing, spreading of epidermal cells  (IEA,ISO)

Cellular Component

References

Additional References at PubMed
PMID:7687426   PMID:7726844   PMID:7897272   PMID:8101453   PMID:8106171   PMID:8668339   PMID:8786091   PMID:9073066   PMID:9111364   PMID:9256341   PMID:9265625   PMID:9373945  
PMID:9522127   PMID:10451362   PMID:10767351   PMID:10831122   PMID:11084035   PMID:11683913   PMID:11763998   PMID:11959851   PMID:12145306   PMID:12145307   PMID:12145310   PMID:12407713  
PMID:12477932   PMID:12750290   PMID:12925529   PMID:14571277   PMID:14671321   PMID:14679154   PMID:15060165   PMID:15489334   PMID:16327884   PMID:16425399   PMID:16467978   PMID:16540516  
PMID:16642368   PMID:17693062   PMID:18029348   PMID:18056036   PMID:18187185   PMID:18299954   PMID:18349132   PMID:18786927   PMID:19147956   PMID:19240061   PMID:19274049   PMID:19407244  
PMID:19453261   PMID:19590514   PMID:19835636   PMID:20004646   PMID:20107842   PMID:20211142   PMID:20301307   PMID:20506112   PMID:20538960   PMID:20572854   PMID:20620318   PMID:20634891  
PMID:20672350   PMID:20682066   PMID:21362336   PMID:21465479   PMID:21471203   PMID:21498730   PMID:21499300   PMID:21512281   PMID:21730974   PMID:21873635   PMID:22332551   PMID:22633971  
PMID:22717651   PMID:22730815   PMID:23275563   PMID:23949913   PMID:24549638   PMID:24666290   PMID:26186194   PMID:26427715   PMID:26786210   PMID:27088357   PMID:28286778   PMID:28473536  
PMID:28514442   PMID:28933666   PMID:29860758   PMID:30341511   PMID:30779868   PMID:31548378   PMID:32210188   PMID:32248833   PMID:32296183   PMID:32393512   PMID:32814053   PMID:33731348  
PMID:33958655   PMID:33961781   PMID:34435915  


Genomics

Comparative Map Data
MSX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh385174,724,582 - 174,730,896 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl5174,724,582 - 174,730,896 (+)EnsemblGRCh38hg38GRCh38
GRCh375174,151,585 - 174,157,899 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 365174,084,181 - 174,090,508 (+)NCBINCBI36hg18NCBI36
Build 345174,084,207 - 174,090,507NCBI
Celera5170,185,579 - 170,191,910 (+)NCBI
Cytogenetic Map5q35.2NCBI
HuRef5169,246,978 - 169,253,303 (+)NCBIHuRef
CHM1_15173,583,988 - 173,590,298 (+)NCBICHM1_1
Msx2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391353,620,917 - 53,626,816 (-)NCBIGRCm39mm39
GRCm39 Ensembl1353,620,920 - 53,627,110 (-)Ensembl
GRCm381353,466,881 - 53,472,780 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1353,466,884 - 53,473,074 (-)EnsemblGRCm38mm10GRCm38
MGSCv371353,562,250 - 53,568,149 (-)NCBIGRCm37mm9NCBIm37
MGSCv361353,475,420 - 53,480,608 (-)NCBImm8
Celera1354,545,172 - 54,551,024 (-)NCBICelera
Cytogenetic Map13B1NCBI
cM Map1327.84NCBI
Msx2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21711,097,214 - 11,102,879 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1711,097,103 - 11,102,879 (+)Ensembl
Rnor_6.01711,683,862 - 11,689,527 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1711,683,862 - 11,689,527 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01713,785,024 - 13,790,689 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41717,243,262 - 17,248,927 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11717,247,335 - 17,247,755 (+)NCBI
Celera1711,158,359 - 11,164,024 (+)NCBICelera
RH 3.4 Map17109.2RGD
Cytogenetic Map17p14NCBI
Msx2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540827,323,360 - 27,329,755 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540827,323,405 - 27,329,484 (+)NCBIChiLan1.0ChiLan1.0
MSX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.15176,968,315 - 176,974,679 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl5176,967,902 - 176,976,609 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v05170,063,137 - 170,070,226 (+)NCBIMhudiblu_PPA_v0panPan3
MSX2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1438,002,724 - 38,007,407 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl438,002,428 - 38,007,407 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha437,948,799 - 37,953,445 (-)NCBI
ROS_Cfam_1.0438,376,184 - 38,380,830 (-)NCBI
ROS_Cfam_1.0 Ensembl438,375,888 - 38,381,225 (-)Ensembl
UMICH_Zoey_3.1438,192,821 - 38,197,476 (-)NCBI
UNSW_CanFamBas_1.0438,380,991 - 38,385,645 (-)NCBI
UU_Cfam_GSD_1.0438,891,167 - 38,895,822 (-)NCBI
Msx2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721392,492,782 - 92,498,921 (-)NCBI
SpeTri2.0NW_0049366091,216,436 - 1,221,528 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MSX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1649,766,897 - 49,771,634 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11649,765,587 - 49,771,745 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
MSX2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12376,873,499 - 76,879,935 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl2376,873,669 - 76,879,553 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660341,717,428 - 1,723,746 (-)NCBIVero_WHO_p1.0
Msx2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473315,288,417 - 15,294,481 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH119225  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375174,153,104 - 174,153,437UniSTSGRCh37
Build 365174,085,710 - 174,086,043RGDNCBI36
Celera5170,187,108 - 170,187,441RGD
Cytogenetic Map5q35.2UniSTS
HuRef5169,248,507 - 169,248,840UniSTS
TNG Radiation Hybrid Map582208.0UniSTS
GDB:266598  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375174,155,856 - 174,156,054UniSTSGRCh37
Build 365174,088,462 - 174,088,660RGDNCBI36
Celera5170,189,861 - 170,190,061RGD
Cytogenetic Map5q35.2UniSTS
HuRef5169,251,260 - 169,251,454UniSTS
PMC164857P2  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371756,234,746 - 56,235,165UniSTSGRCh37
GRCh375174,156,167 - 174,156,586UniSTSGRCh37
Build 365174,088,773 - 174,089,192RGDNCBI36
Celera1752,696,525 - 52,696,944UniSTS
Celera5170,190,174 - 170,190,593RGD
Cytogenetic Map5q35.2UniSTS
Cytogenetic Map17q22UniSTS
HuRef1751,595,564 - 51,595,983UniSTS
HuRef5169,251,567 - 169,251,986UniSTS
MSX2_1676  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375174,156,261 - 174,157,073UniSTSGRCh37
Build 365174,088,867 - 174,089,679RGDNCBI36
Celera5170,190,268 - 170,191,080RGD
HuRef5169,251,661 - 169,252,473UniSTS
SHGC-11995  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh375174,156,626 - 174,156,744UniSTSGRCh37
Build 365174,089,232 - 174,089,350RGDNCBI36
Celera5170,190,633 - 170,190,751RGD
Cytogenetic Map5q35.2UniSTS
HuRef5169,252,026 - 169,252,144UniSTS
Stanford-G3 RH Map56151.0UniSTS
GeneMap99-G3 RH Map56239.0UniSTS
RH79930  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5q35.2UniSTS
GeneMap99-GB4 RH Map5640.67UniSTS
STS-X69295  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map5q35.2UniSTS
GeneMap99-GB4 RH Map5640.77UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:584
Count of miRNA genes:461
Interacting mature miRNAs:489
Transcripts:ENST00000239243, ENST00000507785
Prediction methods:Miranda, Rnahybrid
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
High
Medium 132 350 9 5 3 7 558 25 74 52 321 79 5 4 406 5
Low 1839 1676 731 173 432 31 3555 1979 1817 152 959 1224 151 1 1099 2201 1
Below cutoff 455 440 752 240 430 223 234 179 1692 182 160 262 18 101 180

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_008124 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001363626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_002449 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC117531 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AH004951 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL552909 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC015509 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BT009814 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471062 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068273 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CS406127 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D14970 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D26145 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D31771 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  D89377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S75308 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  S75361 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  W38629 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X69295 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000239243   ⟹   ENSP00000239243
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5174,724,582 - 174,730,896 (+)Ensembl
RefSeq Acc Id: ENST00000507785   ⟹   ENSP00000427425
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl5174,724,602 - 174,729,880 (+)Ensembl
RefSeq Acc Id: NM_001363626   ⟹   NP_001350555
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385174,724,582 - 174,730,896 (+)NCBI
Sequence:
RefSeq Acc Id: NM_002449   ⟹   NP_002440
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh385174,724,582 - 174,730,896 (+)NCBI
GRCh375174,151,575 - 174,157,902 (+)ENTREZGENE
Build 365174,084,181 - 174,090,508 (+)NCBI Archive
HuRef5169,246,978 - 169,253,303 (+)ENTREZGENE
CHM1_15173,583,988 - 173,590,298 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_002440   ⟸   NM_002449
- Peptide Label: isoform 1
- UniProtKB: P35548 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001350555   ⟸   NM_001363626
- Peptide Label: isoform 2
RefSeq Acc Id: ENSP00000427425   ⟸   ENST00000507785
RefSeq Acc Id: ENSP00000239243   ⟸   ENST00000239243

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P35548-F1-model_v2 AlphaFold P35548 1-267 view protein structure

Promoters
RGD ID:6803379
Promoter ID:HG_KWN:51828
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:HeLa_S3
Transcripts:OTTHUMT00000252981
Position:
Human AssemblyChrPosition (strand)Source
Build 365174,083,601 - 174,084,302 (+)MPROMDB
RGD ID:6871600
Promoter ID:EPDNEW_H8964
Type:initiation region
Name:MSX2_1
Description:msh homeobox 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh385174,724,622 - 174,724,682EPDNEW

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_002449.5(MSX2):c.443C>A (p.Pro148His) single nucleotide variant Craniosynostosis 2 [RCV000018474]|Enlarged parietal foramina [RCV001210266] Chr5:174729222 [GRCh38]
Chr5:174156225 [GRCh37]
Chr5:5q35.2
pathogenic
MSX2, 6-BP DEL, NT475 deletion Parietal foramina 1 [RCV000018475] Chr5:5q34-q35 pathogenic
NM_002449.5(MSX2):c.515G>A (p.Arg172His) single nucleotide variant Parietal foramina 1 [RCV000018476] Chr5:174729294 [GRCh38]
Chr5:174156297 [GRCh37]
Chr5:5q35.2
pathogenic
nsv513767 deletion Parietal foramina 1 [RCV000018477] Chr5:5q34-q35 pathogenic
NM_002449.5(MSX2):c.265_266delinsTA (p.Ala89Ter) indel Parietal foramina 1 [RCV000018478] Chr5:174724924..174724925 [GRCh38]
Chr5:174151927..174151928 [GRCh37]
Chr5:5q35.2
pathogenic
NM_002449.5(MSX2):c.345del (p.Ala114_Trp115insTer) deletion Parietal foramina 1 [RCV000018479] Chr5:174725003 [GRCh38]
Chr5:174152006 [GRCh37]
Chr5:5q35.2
pathogenic
NM_002449.5(MSX2):c.505_508dup (p.Ala170fs) duplication Parietal foramina with cleidocranial dysplasia [RCV000018480] Chr5:174729283..174729284 [GRCh38]
Chr5:174156286..174156287 [GRCh37]
Chr5:5q35.2
pathogenic
NM_002449.5(MSX2):c.548_555del (p.Glu183fs) deletion Parietal foramina 1 [RCV000018481] Chr5:174729324..174729331 [GRCh38]
Chr5:174156327..174156334 [GRCh37]
Chr5:5q35.2
pathogenic
GRCh38/hg38 5q32-35.3(chr5:149714592-181272151)x3 copy number gain See cases [RCV000051863] Chr5:149714592..181272151 [GRCh38]
Chr5:149094155..180699152 [GRCh37]
Chr5:149074348..180631758 [NCBI36]
Chr5:5q32-35.3
pathogenic
GRCh38/hg38 5q33.3-35.3(chr5:160029980-181269805)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051865]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051865]|See cases [RCV000051865] Chr5:160029980..181269805 [GRCh38]
Chr5:159456987..180696806 [GRCh37]
Chr5:159389565..180629412 [NCBI36]
Chr5:5q33.3-35.3
pathogenic
GRCh38/hg38 5q34-35.3(chr5:168689326-181269946)x3 copy number gain See cases [RCV000051866] Chr5:168689326..181269946 [GRCh38]
Chr5:168116331..180696947 [GRCh37]
Chr5:168048909..180629553 [NCBI36]
Chr5:5q34-35.3
pathogenic
GRCh38/hg38 5q35.1-35.2(chr5:172961091-175054665)x1 copy number loss See cases [RCV000052150] Chr5:172961091..175054665 [GRCh38]
Chr5:172388094..174481668 [GRCh37]
Chr5:172320700..174414274 [NCBI36]
Chr5:5q35.1-35.2
pathogenic
GRCh38/hg38 5q33.3-35.3(chr5:156825512-181269805)x3 copy number gain See cases [RCV000133847] Chr5:156825512..181269805 [GRCh38]
Chr5:156252523..180696806 [GRCh37]
Chr5:156185101..180629412 [NCBI36]
Chr5:5q33.3-35.3
pathogenic
GRCh38/hg38 5q35.2(chr5:173949773-174900395)x1 copy number loss See cases [RCV000135638] Chr5:173949773..174900395 [GRCh38]
Chr5:173376776..174327398 [GRCh37]
Chr5:173309382..174260004 [NCBI36]
Chr5:5q35.2
pathogenic
GRCh38/hg38 5q34-35.3(chr5:164386701-181269805)x3 copy number gain See cases [RCV000135546] Chr5:164386701..181269805 [GRCh38]
Chr5:163813707..180696806 [GRCh37]
Chr5:163746285..180629412 [NCBI36]
Chr5:5q34-35.3
pathogenic
GRCh38/hg38 5q35.1-35.3(chr5:169334755-181285301)x3 copy number gain See cases [RCV000141249] Chr5:169334755..181285301 [GRCh38]
Chr5:168761759..180712302 [GRCh37]
Chr5:168694337..180644908 [NCBI36]
Chr5:5q35.1-35.3
pathogenic
GRCh38/hg38 5q35.1-35.2(chr5:173237772-176614618)x3 copy number gain See cases [RCV000142647] Chr5:173237772..176614618 [GRCh38]
Chr5:172664775..176041619 [GRCh37]
Chr5:172597381..175974225 [NCBI36]
Chr5:5q35.1-35.2
pathogenic
GRCh38/hg38 5q35.2(chr5:174724141-174742787)x1 copy number loss See cases [RCV000143339] Chr5:174724141..174742787 [GRCh38]
Chr5:174151144..174169790 [GRCh37]
Chr5:174083750..174102396 [NCBI36]
Chr5:5q35.2
pathogenic
NM_002449.5(MSX2):c.-42C>T single nucleotide variant Craniosynostosis 2 [RCV000264746]|Parietal foramina 1 [RCV000359264] Chr5:174724618 [GRCh38]
Chr5:174151621 [GRCh37]
Chr5:5q35.2
benign|likely benign|uncertain significance
NM_002449.5(MSX2):c.*363A>G single nucleotide variant Craniosynostosis 2 [RCV000260056]|Parietal foramina 1 [RCV000375711] Chr5:174729946 [GRCh38]
Chr5:174156949 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.375G>T (p.Pro125=) single nucleotide variant not specified [RCV000194886] Chr5:174725034 [GRCh38]
Chr5:174152037 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.443C>T (p.Pro148Leu) single nucleotide variant Craniosynostosis 2 [RCV000203576]|Enlarged parietal foramina [RCV000690192] Chr5:174729222 [GRCh38]
Chr5:174156225 [GRCh37]
Chr5:5q35.2
pathogenic|likely pathogenic
GRCh37/hg19 5q35.2(chr5:173043321-174953690)x3 copy number gain Ductal breast carcinoma [RCV000207114] Chr5:173043321..174953690 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.360C>T (p.Gly120=) single nucleotide variant Parietal foramina 1 [RCV000525101] Chr5:174725019 [GRCh38]
Chr5:174152022 [GRCh37]
Chr5:5q35.2
likely benign
NM_002449.5(MSX2):c.386T>C (p.Met129Thr) single nucleotide variant Craniosynostosis 2 [RCV000270658]|Enlarged parietal foramina [RCV001513220]|Parietal foramina 1 [RCV000987635]|not provided [RCV001711690]|not specified [RCV000246108] Chr5:174729165 [GRCh38]
Chr5:174156168 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.*510A>G single nucleotide variant Craniosynostosis 2 [RCV000286620]|Parietal foramina 1 [RCV000339309] Chr5:174730093 [GRCh38]
Chr5:174157096 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.*1125A>G single nucleotide variant Craniosynostosis 2 [RCV000280532]|Parietal foramina 1 [RCV000337904] Chr5:174730708 [GRCh38]
Chr5:174157711 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.*46G>T single nucleotide variant Craniosynostosis 2 [RCV000337817]|Parietal foramina 1 [RCV000280472] Chr5:174729629 [GRCh38]
Chr5:174156632 [GRCh37]
Chr5:5q35.2
likely benign|uncertain significance
NM_002449.5(MSX2):c.*349T>C single nucleotide variant Craniosynostosis 2 [RCV000275136]|Parietal foramina 1 [RCV000318732] Chr5:174729932 [GRCh38]
Chr5:174156935 [GRCh37]
Chr5:5q35.2
benign|likely benign
NM_002449.5(MSX2):c.635C>G (p.Ala212Gly) single nucleotide variant Craniosynostosis 2 [RCV000276654]|Parietal foramina 1 [RCV000389679] Chr5:174729414 [GRCh38]
Chr5:174156417 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.*723A>C single nucleotide variant Craniosynostosis 2 [RCV000353287]|Parietal foramina 1 [RCV000300717] Chr5:174730306 [GRCh38]
Chr5:174157309 [GRCh37]
Chr5:5q35.2
benign|likely benign
NM_002449.5(MSX2):c.*416A>C single nucleotide variant Craniosynostosis 2 [RCV000317572]|Parietal foramina 1 [RCV000378679] Chr5:174729999 [GRCh38]
Chr5:174157002 [GRCh37]
Chr5:5q35.2
benign|likely benign
NM_002449.5(MSX2):c.*1249T>C single nucleotide variant Craniosynostosis 2 [RCV000359784]|Parietal foramina 1 [RCV000302601] Chr5:174730832 [GRCh38]
Chr5:174157835 [GRCh37]
Chr5:5q35.2
benign|likely benign
NM_002449.5(MSX2):c.*172G>A single nucleotide variant Craniosynostosis 2 [RCV000346807]|Parietal foramina 1 [RCV000303826] Chr5:174729755 [GRCh38]
Chr5:174156758 [GRCh37]
Chr5:5q35.2
benign|likely benign
NM_002449.5(MSX2):c.*1007T>A single nucleotide variant Craniosynostosis 2 [RCV000288160]|Parietal foramina 1 [RCV000326904] Chr5:174730590 [GRCh38]
Chr5:174157593 [GRCh37]
Chr5:5q35.2
benign|likely benign
NM_002449.5(MSX2):c.*526T>C single nucleotide variant Craniosynostosis 2 [RCV000289882]|Parietal foramina 1 [RCV000377617] Chr5:174730109 [GRCh38]
Chr5:174157112 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.-50C>T single nucleotide variant Craniosynostosis 2 [RCV000304545]|Parietal foramina 1 [RCV000393390] Chr5:174724610 [GRCh38]
Chr5:174151613 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.*1176G>C single nucleotide variant Craniosynostosis 2 [RCV000359850]|Parietal foramina 1 [RCV000393366] Chr5:174730759 [GRCh38]
Chr5:174157762 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.*257T>C single nucleotide variant Craniosynostosis 2 [RCV000397493]|Parietal foramina 1 [RCV000307215] Chr5:174729840 [GRCh38]
Chr5:174156843 [GRCh37]
Chr5:5q35.2
benign|likely benign
NM_002449.5(MSX2):c.*144C>T single nucleotide variant Craniosynostosis 2 [RCV000343515]|Parietal foramina 1 [RCV000405689] Chr5:174729727 [GRCh38]
Chr5:174156730 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.-17C>G single nucleotide variant Craniosynostosis 2 [RCV000365140]|Parietal foramina 1 [RCV000310571]|not provided [RCV001653694] Chr5:174724643 [GRCh38]
Chr5:174151646 [GRCh37]
Chr5:5q35.2
benign|likely benign
NM_002449.5(MSX2):c.*1006dup duplication Craniosynostosis syndrome [RCV000327898]|Enlarged parietal foramina [RCV000384938] Chr5:174730580..174730581 [GRCh38]
Chr5:174157583..174157584 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.*658C>T single nucleotide variant Craniosynostosis 2 [RCV000396378]|Parietal foramina 1 [RCV000368464] Chr5:174730241 [GRCh38]
Chr5:174157244 [GRCh37]
Chr5:5q35.2
benign|likely benign
NM_002449.5(MSX2):c.*647C>T single nucleotide variant Craniosynostosis 2 [RCV000404786]|Parietal foramina 1 [RCV000311469] Chr5:174730230 [GRCh38]
Chr5:174157233 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.*1096A>G single nucleotide variant Craniosynostosis 2 [RCV000349154]|Parietal foramina 1 [RCV000406371] Chr5:174730679 [GRCh38]
Chr5:174157682 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.*1146T>C single nucleotide variant Craniosynostosis 2 [RCV000403211]|Parietal foramina 1 [RCV000298013] Chr5:174730729 [GRCh38]
Chr5:174157732 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.699G>A (p.Ala233=) single nucleotide variant Craniosynostosis 2 [RCV000331763]|Parietal foramina 1 [RCV000542377] Chr5:174729478 [GRCh38]
Chr5:174156481 [GRCh37]
Chr5:5q35.2
benign|likely benign
NM_002449.5(MSX2):c.*1312A>G single nucleotide variant Craniosynostosis 2 [RCV000272150]|Parietal foramina 1 [RCV000329321] Chr5:174730895 [GRCh38]
Chr5:174157898 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.*863A>G single nucleotide variant Craniosynostosis 2 [RCV000260811]|Parietal foramina 1 [RCV000324500] Chr5:174730446 [GRCh38]
Chr5:174157449 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.*289A>G single nucleotide variant Craniosynostosis 2 [RCV000364259]|Parietal foramina 1 [RCV000276383] Chr5:174729872 [GRCh38]
Chr5:174156875 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.*946T>G single nucleotide variant Craniosynostosis 2 [RCV000358161]|Parietal foramina 1 [RCV000265716] Chr5:174730529 [GRCh38]
Chr5:174157532 [GRCh37]
Chr5:5q35.2
uncertain significance
GRCh37/hg19 5q15-35.3(chr5:94844077-178830410)x3 copy number gain not provided [RCV000487658] Chr5:94844077..178830410 [GRCh37]
Chr5:5q15-35.3
likely benign
NM_002449.5(MSX2):c.*306G>T single nucleotide variant Craniosynostosis 2 [RCV000367369]|Parietal foramina 1 [RCV000315104] Chr5:174729889 [GRCh38]
Chr5:174156892 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.*530A>G single nucleotide variant Craniosynostosis 2 [RCV000403936]|Parietal foramina 1 [RCV000347144] Chr5:174730113 [GRCh38]
Chr5:174157116 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.*102C>T single nucleotide variant Craniosynostosis 2 [RCV000286224]|Parietal foramina 1 [RCV000371419] Chr5:174729685 [GRCh38]
Chr5:174156688 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.*1086dup duplication Craniosynostosis syndrome [RCV000388421]|Enlarged parietal foramina [RCV000296539] Chr5:174730663..174730664 [GRCh38]
Chr5:174157666..174157667 [GRCh37]
Chr5:5q35.2
likely benign
NM_002449.5(MSX2):c.*601C>T single nucleotide variant Craniosynostosis 2 [RCV000288658]|Parietal foramina 1 [RCV000351073] Chr5:174730184 [GRCh38]
Chr5:174157187 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.*512G>T single nucleotide variant Craniosynostosis 2 [RCV001151927]|Parietal foramina 1 [RCV001151928] Chr5:174730095 [GRCh38]
Chr5:174157098 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.514C>G (p.Arg172Gly) single nucleotide variant not provided [RCV000585463] Chr5:174729293 [GRCh38]
Chr5:174156296 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.*1050T>C single nucleotide variant Craniosynostosis 2 [RCV001152033]|Parietal foramina 1 [RCV001152032] Chr5:174730633 [GRCh38]
Chr5:174157636 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.*157A>T single nucleotide variant Craniosynostosis 2 [RCV001151846]|Parietal foramina 1 [RCV001151845] Chr5:174729740 [GRCh38]
Chr5:174156743 [GRCh37]
Chr5:5q35.2
benign
GRCh37/hg19 5p15.33-q35.3(chr5:113577-180719789) copy number gain See cases [RCV000510723] Chr5:113577..180719789 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
GRCh37/hg19 5q21.3-35.3(chr5:106716357-180687338)x3 copy number gain See cases [RCV000448245] Chr5:106716357..180687338 [GRCh37]
Chr5:5q21.3-35.3
pathogenic
GRCh37/hg19 5q35.1-35.3(chr5:171396359-180719789)x3 copy number gain See cases [RCV000448458] Chr5:171396359..180719789 [GRCh37]
Chr5:5q35.1-35.3
pathogenic
GRCh37/hg19 5q35.1-35.3(chr5:172031248-180719789)x3 copy number gain See cases [RCV000512068] Chr5:172031248..180719789 [GRCh37]
Chr5:5q35.1-35.3
pathogenic
GRCh37/hg19 5p15.1-q35.2(chr5:17628741-176575720)x1 copy number loss See cases [RCV000511978] Chr5:17628741..176575720 [GRCh37]
Chr5:5p15.1-q35.2
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:113577-180719789)x3 copy number gain See cases [RCV000512039] Chr5:113577..180719789 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
NM_002449.5(MSX2):c.698C>T (p.Ala233Val) single nucleotide variant Enlarged parietal foramina [RCV000644909] Chr5:174729477 [GRCh38]
Chr5:174156480 [GRCh37]
Chr5:5q35.2
uncertain significance
GRCh37/hg19 5q35.2(chr5:174070065-174601039)x3 copy number gain not provided [RCV000682613] Chr5:174070065..174601039 [GRCh37]
Chr5:5q35.2
uncertain significance
GRCh37/hg19 5p15.33-q35.3(chr5:25328-180693344)x3 copy number gain not provided [RCV000744323] Chr5:25328..180693344 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
GRCh37/hg19 5p15.33-q35.3(chr5:13648-180905029)x3 copy number gain not provided [RCV000744317] Chr5:13648..180905029 [GRCh37]
Chr5:5p15.33-q35.3
pathogenic
GRCh37/hg19 5q33.2-35.3(chr5:155344802-180693344)x3 copy number gain not provided [RCV000745284] Chr5:155344802..180693344 [GRCh37]
Chr5:5q33.2-35.3
pathogenic
GRCh37/hg19 5q35.2(chr5:174130513-174193309)x3 copy number gain not provided [RCV000745334] Chr5:174130513..174193309 [GRCh37]
Chr5:5q35.2
benign
Single allele duplication not provided [RCV001691163] Chr5:174724439..174724440 [GRCh38]
Chr5:174151442..174151443 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.379+68C>T single nucleotide variant not provided [RCV001708748] Chr5:174725106 [GRCh38]
Chr5:174152109 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.803A>G (p.Ter268=) single nucleotide variant Enlarged parietal foramina [RCV001478215]|not provided [RCV000938412] Chr5:174729582 [GRCh38]
Chr5:174156585 [GRCh37]
Chr5:5q35.2
likely benign
NM_002449.5(MSX2):c.723G>A (p.Pro241=) single nucleotide variant Enlarged parietal foramina [RCV002064508]|not provided [RCV000864904] Chr5:174729502 [GRCh38]
Chr5:174156505 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.442C>T (p.Pro148Ser) single nucleotide variant Enlarged parietal foramina [RCV000792855] Chr5:174729221 [GRCh38]
Chr5:174156224 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.255C>T (p.Gly85=) single nucleotide variant Enlarged parietal foramina [RCV000804878] Chr5:174724914 [GRCh38]
Chr5:174151917 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.380-9G>C single nucleotide variant not provided [RCV000960701] Chr5:174729150 [GRCh38]
Chr5:174156153 [GRCh37]
Chr5:5q35.2
likely benign
NM_002449.5(MSX2):c.-56C>A single nucleotide variant Craniosynostosis 2 [RCV001151732]|Parietal foramina 1 [RCV001151733] Chr5:174724604 [GRCh38]
Chr5:174151607 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.*106C>T single nucleotide variant Craniosynostosis 2 [RCV001151842]|Parietal foramina 1 [RCV001151841] Chr5:174729689 [GRCh38]
Chr5:174156692 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.380-164G>A single nucleotide variant Parietal foramina 1 [RCV000987634]|not provided [RCV001619870] Chr5:174728995 [GRCh38]
Chr5:174155998 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.*1178C>T single nucleotide variant Craniosynostosis 2 [RCV001155903]|Parietal foramina 1 [RCV001155904] Chr5:174730761 [GRCh38]
Chr5:174157764 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.*878C>T single nucleotide variant Craniosynostosis 2 [RCV001157504]|Parietal foramina 1 [RCV001157503] Chr5:174730461 [GRCh38]
Chr5:174157464 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.*1206T>C single nucleotide variant Craniosynostosis 2 [RCV001157606]|Parietal foramina 1 [RCV001157607] Chr5:174730789 [GRCh38]
Chr5:174157792 [GRCh37]
Chr5:5q35.2
benign|likely benign
NM_002449.5(MSX2):c.*1233T>C single nucleotide variant Craniosynostosis 2 [RCV001157608]|Parietal foramina 1 [RCV001157609] Chr5:174730816 [GRCh38]
Chr5:174157819 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.793C>T (p.His265Tyr) single nucleotide variant Craniosynostosis 2 [RCV001197937] Chr5:174729572 [GRCh38]
Chr5:174156575 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.315G>C (p.Lys105Asn) single nucleotide variant Craniosynostosis 2 [RCV001155621]|Parietal foramina 1 [RCV001155622] Chr5:174724974 [GRCh38]
Chr5:174151977 [GRCh37]
Chr5:5q35.2
benign|likely benign
NM_002449.5(MSX2):c.*366T>G single nucleotide variant Craniosynostosis 2 [RCV001155703]|Parietal foramina 1 [RCV001155704] Chr5:174729949 [GRCh38]
Chr5:174156952 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.380-305C>T single nucleotide variant not provided [RCV001570988] Chr5:174728854 [GRCh38]
Chr5:174155857 [GRCh37]
Chr5:5q35.2
likely benign
Single allele duplication not provided [RCV001650693] Chr5:174724413..174724414 [GRCh38]
Chr5:174151416..174151417 [GRCh37]
Chr5:5q35.2
benign
Single allele duplication not provided [RCV001720942] Chr5:174724439..174724440 [GRCh38]
Chr5:174151442..174151443 [GRCh37]
Chr5:5q35.2
benign
Single allele deletion not provided [RCV001615520] Chr5:174724414 [GRCh38]
Chr5:174151417 [GRCh37]
Chr5:5q35.2
benign
Single allele duplication not provided [RCV001679978] Chr5:174724413..174724414 [GRCh38]
Chr5:174151416..174151417 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.379+59G>A single nucleotide variant not provided [RCV001641999] Chr5:174725097 [GRCh38]
Chr5:174152100 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.380-166G>A single nucleotide variant not provided [RCV001586471] Chr5:174728993 [GRCh38]
Chr5:174155996 [GRCh37]
Chr5:5q35.2
likely benign
Single allele duplication not provided [RCV001718106] Chr5:174724413..174724414 [GRCh38]
Chr5:174151416..174151417 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.379+274G>A single nucleotide variant not provided [RCV001594173] Chr5:174725312 [GRCh38]
Chr5:174152315 [GRCh37]
Chr5:5q35.2
likely benign
NM_002449.5(MSX2):c.380-162A>G single nucleotide variant not provided [RCV001557933] Chr5:174728997 [GRCh38]
Chr5:174156000 [GRCh37]
Chr5:5q35.2
likely benign
NM_002449.5(MSX2):c.*465C>T single nucleotide variant Craniosynostosis 2 [RCV001157396]|Parietal foramina 1 [RCV001157397] Chr5:174730048 [GRCh38]
Chr5:174157051 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.495G>A (p.Gln165=) single nucleotide variant not provided [RCV000913863] Chr5:174729274 [GRCh38]
Chr5:174156277 [GRCh37]
Chr5:5q35.2
likely benign
NM_002449.5(MSX2):c.380-191TG[13] microsatellite not provided [RCV001570428] Chr5:174728968..174728969 [GRCh38]
Chr5:174155971..174155972 [GRCh37]
Chr5:5q35.2
likely benign
NM_002449.5(MSX2):c.379+69C>T single nucleotide variant not provided [RCV001654951] Chr5:174725107 [GRCh38]
Chr5:174152110 [GRCh37]
Chr5:5q35.2
benign
Single allele deletion not provided [RCV001608504] Chr5:174724439 [GRCh38]
Chr5:174151442 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.380-191TG[11] microsatellite not provided [RCV001598911] Chr5:174728968..174728973 [GRCh38]
Chr5:174155971..174155976 [GRCh37]
Chr5:5q35.2
benign
Single allele insertion not provided [RCV001638487] Chr5:174724412..174724413 [GRCh38]
Chr5:174151415..174151416 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.*644C>T single nucleotide variant Craniosynostosis 2 [RCV001155801]|Parietal foramina 1 [RCV001155800] Chr5:174730227 [GRCh38]
Chr5:174157230 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.751C>T (p.Pro251Ser) single nucleotide variant Craniosynostosis 2 [RCV001157290]|Parietal foramina 1 [RCV001157289] Chr5:174729530 [GRCh38]
Chr5:174156533 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.*466G>A single nucleotide variant Craniosynostosis 2 [RCV001157399]|Parietal foramina 1 [RCV001157398] Chr5:174730049 [GRCh38]
Chr5:174157052 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.*126T>C single nucleotide variant Craniosynostosis 2 [RCV001151844]|Parietal foramina 1 [RCV001151843] Chr5:174729709 [GRCh38]
Chr5:174156712 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.*516A>G single nucleotide variant Craniosynostosis 2 [RCV001151930]|Parietal foramina 1 [RCV001151929] Chr5:174730099 [GRCh38]
Chr5:174157102 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.122A>T (p.Lys41Met) single nucleotide variant Craniosynostosis 2 [RCV001152972]|Parietal foramina 1 [RCV001152973] Chr5:174724781 [GRCh38]
Chr5:174151784 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.286G>T (p.Val96Leu) single nucleotide variant Craniosynostosis 2 [RCV001152974]|Enlarged parietal foramina [RCV002032410]|Parietal foramina 1 [RCV001152975]|not specified [RCV001819860] Chr5:174724945 [GRCh38]
Chr5:174151948 [GRCh37]
Chr5:5q35.2
likely benign|uncertain significance
NM_002449.5(MSX2):c.*183G>T single nucleotide variant Craniosynostosis 2 [RCV001153087]|Parietal foramina 1 [RCV001153086] Chr5:174729766 [GRCh38]
Chr5:174156769 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.*635G>A single nucleotide variant Craniosynostosis 2 [RCV001153195]|Parietal foramina 1 [RCV001153194] Chr5:174730218 [GRCh38]
Chr5:174157221 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.*601C>G single nucleotide variant Craniosynostosis 2 [RCV001153192]|Parietal foramina 1 [RCV001153193] Chr5:174730184 [GRCh38]
Chr5:174157187 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.*1064A>G single nucleotide variant Craniosynostosis 2 [RCV001152034]|Parietal foramina 1 [RCV001152035] Chr5:174730647 [GRCh38]
Chr5:174157650 [GRCh37]
Chr5:5q35.2
uncertain significance
Single allele deletion not provided [RCV001669205] Chr5:174724414..174724415 [GRCh38]
Chr5:174151417..174151418 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.380-160_380-159del microsatellite not provided [RCV001685873] Chr5:174728996..174728997 [GRCh38]
Chr5:174155999..174156000 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.380-163TA[3] microsatellite not provided [RCV001685577] Chr5:174728995..174728996 [GRCh38]
Chr5:174155998..174155999 [GRCh37]
Chr5:5q35.2
benign
Single allele single nucleotide variant not provided [RCV001682385] Chr5:174724413 [GRCh38]
Chr5:174151416 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.*1189G>A single nucleotide variant Craniosynostosis 2 [RCV001155905]|Parietal foramina 1 [RCV001155906] Chr5:174730772 [GRCh38]
Chr5:174157775 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.304G>A (p.Ala102Thr) single nucleotide variant Craniosynostosis 2 [RCV001152977]|Parietal foramina 1 [RCV001152976] Chr5:174724963 [GRCh38]
Chr5:174151966 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.*1161C>T single nucleotide variant Craniosynostosis 2 [RCV001153306]|Parietal foramina 1 [RCV001153305] Chr5:174730744 [GRCh38]
Chr5:174157747 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.698dup (p.Ser234fs) duplication Craniosynostosis 2 [RCV001197187] Chr5:174729476..174729477 [GRCh38]
Chr5:174156479..174156480 [GRCh37]
Chr5:5q35.2
uncertain significance
GRCh37/hg19 5q35.2(chr5:173830823-174344055)x3 copy number gain not provided [RCV001259929] Chr5:173830823..174344055 [GRCh37]
Chr5:5q35.2
uncertain significance
GRCh37/hg19 5q35.1-35.3(chr5:170805664-180719789)x3 copy number gain 5q35 microduplication syndrome [RCV001263227] Chr5:170805664..180719789 [GRCh37]
Chr5:5q35.1-35.3
pathogenic
NM_002449.5(MSX2):c.745A>G (p.Ile249Val) single nucleotide variant Enlarged parietal foramina [RCV001298842] Chr5:174729524 [GRCh38]
Chr5:174156527 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.572A>G (p.Gln191Arg) single nucleotide variant not provided [RCV001357858] Chr5:174729351 [GRCh38]
Chr5:174156354 [GRCh37]
Chr5:5q35.2
uncertain significance
Single allele single nucleotide variant not provided [RCV001534295] Chr5:174724464 [GRCh38]
Chr5:174151467 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.380-191TG[12] microsatellite not provided [RCV001614979] Chr5:174728968..174728971 [GRCh38]
Chr5:174155971..174155974 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.380-48T>A single nucleotide variant not provided [RCV001537102] Chr5:174729111 [GRCh38]
Chr5:174156114 [GRCh37]
Chr5:5q35.2
benign
Single allele duplication not provided [RCV001616145] Chr5:174724439..174724440 [GRCh38]
Chr5:174151442..174151443 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.379+8C>G single nucleotide variant Enlarged parietal foramina [RCV001428105] Chr5:174725046 [GRCh38]
Chr5:174152049 [GRCh37]
Chr5:5q35.2
likely benign
NM_002449.5(MSX2):c.577C>T (p.Arg193Ter) single nucleotide variant not provided [RCV001727343] Chr5:174729356 [GRCh38]
Chr5:174156359 [GRCh37]
Chr5:5q35.2
likely pathogenic
NM_002449.5(MSX2):c.380-191TG[9] microsatellite not provided [RCV001776508] Chr5:174728968..174728977 [GRCh38]
Chr5:174155971..174155980 [GRCh37]
Chr5:5q35.2
likely benign
NM_002449.5(MSX2):c.749C>T (p.Pro250Leu) single nucleotide variant Enlarged parietal foramina [RCV001971581] Chr5:174729528 [GRCh38]
Chr5:174156531 [GRCh37]
Chr5:5q35.2
uncertain significance
GRCh37/hg19 5q35.2(chr5:174147094-174200503)x1 copy number loss not provided [RCV001827833] Chr5:174147094..174200503 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.457C>T (p.Gln153Ter) single nucleotide variant Enlarged parietal foramina [RCV001949945] Chr5:174729236 [GRCh38]
Chr5:174156239 [GRCh37]
Chr5:5q35.2
pathogenic
NM_002449.5(MSX2):c.484C>T (p.Arg162Cys) single nucleotide variant Enlarged parietal foramina [RCV001895407] Chr5:174729263 [GRCh38]
Chr5:174156266 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.77C>T (p.Pro26Leu) single nucleotide variant Enlarged parietal foramina [RCV001863829] Chr5:174724736 [GRCh38]
Chr5:174151739 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.505A>G (p.Ile169Val) single nucleotide variant Enlarged parietal foramina [RCV001874279] Chr5:174729284 [GRCh38]
Chr5:174156287 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.152C>T (p.Ala51Val) single nucleotide variant Enlarged parietal foramina [RCV001912364] Chr5:174724811 [GRCh38]
Chr5:174151814 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.143G>C (p.Ser48Thr) single nucleotide variant Enlarged parietal foramina [RCV001912092] Chr5:174724802 [GRCh38]
Chr5:174151805 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.95A>T (p.Glu32Val) single nucleotide variant Enlarged parietal foramina [RCV001993595] Chr5:174724754 [GRCh38]
Chr5:174151757 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.178A>C (p.Lys60Gln) single nucleotide variant Enlarged parietal foramina [RCV001992775] Chr5:174724837 [GRCh38]
Chr5:174151840 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.428G>A (p.Arg143Gln) single nucleotide variant Enlarged parietal foramina [RCV001996470] Chr5:174729207 [GRCh38]
Chr5:174156210 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.449C>G (p.Thr150Ser) single nucleotide variant Enlarged parietal foramina [RCV001878775] Chr5:174729228 [GRCh38]
Chr5:174156231 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.179A>C (p.Lys60Thr) single nucleotide variant Enlarged parietal foramina [RCV001876607] Chr5:174724838 [GRCh38]
Chr5:174151841 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.83C>T (p.Pro28Leu) single nucleotide variant Enlarged parietal foramina [RCV001898133] Chr5:174724742 [GRCh38]
Chr5:174151745 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.712G>A (p.Ala238Thr) single nucleotide variant Enlarged parietal foramina [RCV001957221] Chr5:174729491 [GRCh38]
Chr5:174156494 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.22A>C (p.Asn8His) single nucleotide variant Enlarged parietal foramina [RCV001993685] Chr5:174724681 [GRCh38]
Chr5:174151684 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.103G>C (p.Ala35Pro) single nucleotide variant not provided [RCV002224853] Chr5:174724762 [GRCh38]
Chr5:174151765 [GRCh37]
Chr5:5q35.2
uncertain significance
NM_002449.5(MSX2):c.49G>A (p.Gly17Ser) single nucleotide variant Enlarged parietal foramina [RCV002206890] Chr5:174724708 [GRCh38]
Chr5:174151711 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.174G>A (p.Pro58=) single nucleotide variant Enlarged parietal foramina [RCV002191774] Chr5:174724833 [GRCh38]
Chr5:174151836 [GRCh37]
Chr5:5q35.2
likely benign
NM_002449.5(MSX2):c.750G>A (p.Pro250=) single nucleotide variant Enlarged parietal foramina [RCV002152508] Chr5:174729529 [GRCh38]
Chr5:174156532 [GRCh37]
Chr5:5q35.2
likely benign
NM_002449.5(MSX2):c.252C>T (p.His84=) single nucleotide variant Enlarged parietal foramina [RCV002079754] Chr5:174724911 [GRCh38]
Chr5:174151914 [GRCh37]
Chr5:5q35.2
likely benign
NM_002449.5(MSX2):c.380-18C>G single nucleotide variant Enlarged parietal foramina [RCV002196298] Chr5:174729141 [GRCh38]
Chr5:174156144 [GRCh37]
Chr5:5q35.2
likely benign
NM_002449.5(MSX2):c.228G>A (p.Leu76=) single nucleotide variant Enlarged parietal foramina [RCV002079048] Chr5:174724887 [GRCh38]
Chr5:174151890 [GRCh37]
Chr5:5q35.2
likely benign
NM_002449.5(MSX2):c.117C>T (p.Arg39=) single nucleotide variant Enlarged parietal foramina [RCV002151737] Chr5:174724776 [GRCh38]
Chr5:174151779 [GRCh37]
Chr5:5q35.2
benign
NM_002449.5(MSX2):c.379+7G>C single nucleotide variant Enlarged parietal foramina [RCV002079845] Chr5:174725045 [GRCh38]
Chr5:174152048 [GRCh37]
Chr5:5q35.2
likely benign
NM_002449.5(MSX2):c.379+9G>A single nucleotide variant Enlarged parietal foramina [RCV002103663] Chr5:174725047 [GRCh38]
Chr5:174152050 [GRCh37]
Chr5:5q35.2
likely benign
NM_002449.5(MSX2):c.756G>A (p.Val252=) single nucleotide variant Enlarged parietal foramina [RCV002216838] Chr5:174729535 [GRCh38]
Chr5:174156538 [GRCh37]
Chr5:5q35.2
benign

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:7392 AgrOrtholog
COSMIC MSX2 COSMIC
Ensembl Genes ENSG00000120149 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000239243 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000427425 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENST00000239243 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000507785 ENTREZGENE, UniProtKB/TrEMBL
GTEx ENSG00000120149 GTEx
HGNC ID HGNC:7392 ENTREZGENE
Human Proteome Map MSX2 Human Proteome Map
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot
  Homeobox_CS UniProtKB/Swiss-Prot
  Homeobox_dom UniProtKB/Swiss-Prot
  Homeobox_metazoa UniProtKB/Swiss-Prot
KEGG Report hsa:4488 UniProtKB/Swiss-Prot
NCBI Gene 4488 ENTREZGENE
OMIM 123101 OMIM
  168500 OMIM
  168550 OMIM
  604757 OMIM
Pfam Homeodomain UniProtKB/Swiss-Prot
PharmGKB PA31197 PharmGKB
PRINTS HOMEOBOX UniProtKB/Swiss-Prot
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot
  HOMEOBOX_2 UniProtKB/Swiss-Prot
SMART HOX UniProtKB/Swiss-Prot
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot
UniProt D6RIS4_HUMAN UniProtKB/TrEMBL
  MSX2_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary D3DQN1 UniProtKB/Swiss-Prot
  Q53XM4 UniProtKB/Swiss-Prot
  Q9UD60 UniProtKB/Swiss-Prot