CLSTN3 (calsyntenin 3) - Rat Genome Database

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Gene: CLSTN3 (calsyntenin 3) Homo sapiens
Analyze
Symbol: CLSTN3
Name: calsyntenin 3
RGD ID: 732033
HGNC Page HGNC
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in positive regulation of synapse assembly and positive regulation of synaptic transmission. Predicted to act upstream of or within several processes, including chemical synaptic transmission; positive regulation of protein localization to synapse; and synapse assembly. Predicted to be located in postsynaptic density. Predicted to be part of protein-containing complex. Predicted to be active in cell surface; glutamatergic synapse; and postsynaptic membrane. Predicted to be integral component of postsynaptic density membrane; INTERACTS WITH acrylamide; all-trans-retinoic acid; antirheumatic drug.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: alc-beta; alcadein beta; alcadein-beta; alcbeta; cadherin-related family member 14; calsyntenin-3; CDHR14; CSTN3; KIAA0726; MGC131797; MGC138488
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 Ensembl127,129,698 - 7,158,945 (+)EnsemblGRCh38hg38GRCh38
GRCh38127,130,371 - 7,158,945 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37127,282,967 - 7,311,541 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36127,174,234 - 7,202,808 (+)NCBINCBI36hg18NCBI36
Build 34127,174,236 - 7,201,985NCBI
Celera128,859,131 - 8,887,704 (+)NCBI
Cytogenetic Map12p13.31NCBI
HuRef127,095,705 - 7,124,262 (+)NCBIHuRef
CHM1_1127,281,942 - 7,310,507 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
1. GOA_HUMAN data from the GO Consortium
2. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9872452   PMID:12477932   PMID:12498782   PMID:12972431   PMID:15037614   PMID:15489334   PMID:16344560   PMID:21873635   PMID:22658674   PMID:23376485   PMID:23499467   PMID:25352602  
PMID:26213366   PMID:28514442   PMID:28986522   PMID:31073040   PMID:32296183  


Genomics

Comparative Map Data
CLSTN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl127,129,698 - 7,158,945 (+)EnsemblGRCh38hg38GRCh38
GRCh38127,130,371 - 7,158,945 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37127,282,967 - 7,311,541 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36127,174,234 - 7,202,808 (+)NCBINCBI36hg18NCBI36
Build 34127,174,236 - 7,201,985NCBI
Celera128,859,131 - 8,887,704 (+)NCBI
Cytogenetic Map12p13.31NCBI
HuRef127,095,705 - 7,124,262 (+)NCBIHuRef
CHM1_1127,281,942 - 7,310,507 (+)NCBICHM1_1
Clstn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396124,407,715 - 124,441,743 (-)NCBIGRCm39mm39
GRCm39 Ensembl6124,407,540 - 124,441,753 (-)Ensembl
GRCm386124,430,756 - 124,464,784 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6124,430,581 - 124,464,794 (-)EnsemblGRCm38mm10GRCm38
MGSCv376124,380,774 - 124,414,802 (-)NCBIGRCm37mm9NCBIm37
MGSCv366124,396,386 - 124,430,343 (-)NCBImm8
Celera6126,121,281 - 126,154,711 (-)NCBICelera
Cytogenetic Map6F2NCBI
Clstn3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24157,331,494 - 157,364,769 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl4157,331,494 - 157,364,769 (-)Ensembl
Rnor_6.04157,044,736 - 157,078,013 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4157,043,925 - 157,078,130 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04224,064,529 - 224,097,591 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44160,631,047 - 160,665,193 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14160,875,982 - 160,910,129 (-)NCBI
Celera4146,072,428 - 146,105,625 (-)NCBICelera
Cytogenetic Map4q42NCBI
Clstn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554134,690,637 - 4,719,929 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554134,690,637 - 4,719,929 (+)NCBIChiLan1.0ChiLan1.0
CLSTN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1127,175,951 - 7,204,526 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl127,175,951 - 7,204,526 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0127,260,361 - 7,288,903 (+)NCBIMhudiblu_PPA_v0panPan3
CLSTN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12737,879,047 - 37,913,317 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2737,879,269 - 37,913,281 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha278,703,426 - 8,737,782 (+)NCBI
ROS_Cfam_1.02738,232,299 - 38,265,672 (-)NCBI
UMICH_Zoey_3.12738,106,420 - 38,140,738 (-)NCBI
UNSW_CanFamBas_1.02738,147,404 - 38,181,685 (-)NCBI
UU_Cfam_GSD_1.0278,181,467 - 8,215,782 (+)NCBI
Clstn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945101,963,756 - 102,005,760 (-)NCBI
SpeTri2.0NW_004936709641,615 - 673,309 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLSTN3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl563,572,062 - 63,610,618 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1563,572,062 - 63,612,177 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2565,899,699 - 65,927,179 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CLSTN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1117,197,725 - 7,226,479 (+)NCBI
ChlSab1.1 Ensembl117,197,539 - 7,226,651 (+)Ensembl
Vero_WHO_p1.0NW_023666063984,091 - 1,012,812 (-)NCBI
Clstn3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248603,710,121 - 3,737,617 (+)NCBI

Position Markers
RH103815  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37127,282,130 - 7,282,268UniSTSGRCh37
Build 36127,173,397 - 7,173,535RGDNCBI36
Celera128,858,295 - 8,858,433RGD
Cytogenetic Map12p13.31UniSTS
HuRef127,094,875 - 7,095,013UniSTS
GeneMap99-GB4 RH Map1245.78UniSTS
D12S931  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37127,293,791 - 7,293,943UniSTSGRCh37
Build 36127,185,058 - 7,185,210RGDNCBI36
Celera128,869,954 - 8,870,106RGD
Cytogenetic Map12p13.31UniSTS
HuRef127,106,520 - 7,106,672UniSTS

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:4720
Count of miRNA genes:1067
Interacting mature miRNAs:1356
Transcripts:ENST00000266546, ENST00000331148, ENST00000534830, ENST00000535313, ENST00000535452, ENST00000535668, ENST00000537408, ENST00000538933, ENST00000539982, ENST00000540931, ENST00000541667, ENST00000541770, ENST00000541953, ENST00000542663, ENST00000544584, ENST00000545663
Prediction methods:Microtar, Miranda, 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 1876 1724 1682 581 1681 447 3031 823 3191 357 1201 1565 148 1193 1593 1
Low 555 1260 42 41 263 18 1318 1369 523 62 246 48 24 11 1195 3
Below cutoff 3 4 2 1 6 8 3 15 9 2 1 1 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_014718 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006719163 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AA864252 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB018269 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC018653 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ277460 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK299177 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK299246 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK316059 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY753302 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC039075 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC104767 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC111491 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC112283 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC148258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471116 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DA092023 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KF455598 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000266546   ⟹   ENSP00000266546
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl127,130,371 - 7,158,945 (+)Ensembl
RefSeq Acc Id: ENST00000331148   ⟹   ENSP00000497486
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl127,155,905 - 7,158,945 (+)Ensembl
RefSeq Acc Id: ENST00000534830   ⟹   ENSP00000443490
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl127,131,320 - 7,135,518 (+)Ensembl
RefSeq Acc Id: ENST00000535313   ⟹   ENSP00000496782
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl127,155,868 - 7,158,305 (+)Ensembl
RefSeq Acc Id: ENST00000535452   ⟹   ENSP00000443468
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl127,131,088 - 7,135,443 (+)Ensembl
RefSeq Acc Id: ENST00000535668
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl127,136,301 - 7,138,815 (+)Ensembl
RefSeq Acc Id: ENST00000537408
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl127,132,386 - 7,158,932 (+)Ensembl
RefSeq Acc Id: ENST00000538933
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl127,132,905 - 7,133,913 (+)Ensembl
RefSeq Acc Id: ENST00000539982   ⟹   ENSP00000442801
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl127,131,786 - 7,135,524 (+)Ensembl
RefSeq Acc Id: ENST00000540931
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl127,135,449 - 7,137,315 (+)Ensembl
RefSeq Acc Id: ENST00000541667
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl127,130,428 - 7,136,844 (+)Ensembl
RefSeq Acc Id: ENST00000541770
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl127,143,138 - 7,149,689 (+)Ensembl
RefSeq Acc Id: ENST00000541953   ⟹   ENSP00000443959
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl127,129,698 - 7,135,345 (+)Ensembl
RefSeq Acc Id: ENST00000542663
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl127,150,523 - 7,151,150 (+)Ensembl
RefSeq Acc Id: ENST00000544584
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl127,138,682 - 7,143,198 (+)Ensembl
RefSeq Acc Id: ENST00000545663   ⟹   ENSP00000442612
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl127,130,755 - 7,135,481 (+)Ensembl
RefSeq Acc Id: NM_014718   ⟹   NP_055533
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38127,130,371 - 7,158,945 (+)NCBI
GRCh37127,281,681 - 7,311,541 (+)NCBI
Build 36127,174,234 - 7,202,808 (+)NCBI Archive
Celera128,859,131 - 8,887,704 (+)RGD
HuRef127,095,705 - 7,124,262 (+)RGD
CHM1_1127,281,942 - 7,310,507 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006719163   ⟹   XP_006719226
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38127,131,355 - 7,158,945 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_055533   ⟸   NM_014718
- Peptide Label: precursor
- UniProtKB: Q9BQT9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006719226   ⟸   XM_006719163
- Peptide Label: isoform X1
- UniProtKB: Q9BQT9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000266546   ⟸   ENST00000266546
RefSeq Acc Id: ENSP00000443959   ⟸   ENST00000541953
RefSeq Acc Id: ENSP00000497486   ⟸   ENST00000331148
RefSeq Acc Id: ENSP00000442612   ⟸   ENST00000545663
RefSeq Acc Id: ENSP00000443490   ⟸   ENST00000534830
RefSeq Acc Id: ENSP00000443468   ⟸   ENST00000535452
RefSeq Acc Id: ENSP00000496782   ⟸   ENST00000535313
RefSeq Acc Id: ENSP00000442801   ⟸   ENST00000539982
Protein Domains
CA   Cadherin

Promoters
RGD ID:7223015
Promoter ID:EPDNEW_H17253
Type:multiple initiation site
Name:CLSTN3_4
Description:calsyntenin 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H17255  EPDNEW_H17256  EPDNEW_H17257  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38127,129,207 - 7,129,267EPDNEW
RGD ID:7223019
Promoter ID:EPDNEW_H17255
Type:initiation region
Name:CLSTN3_2
Description:calsyntenin 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H17253  EPDNEW_H17256  EPDNEW_H17257  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38127,130,371 - 7,130,431EPDNEW
RGD ID:7223021
Promoter ID:EPDNEW_H17256
Type:multiple initiation site
Name:CLSTN3_1
Description:calsyntenin 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H17253  EPDNEW_H17255  EPDNEW_H17257  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38127,132,453 - 7,132,513EPDNEW
RGD ID:7223023
Promoter ID:EPDNEW_H17257
Type:initiation region
Name:CLSTN3_3
Description:calsyntenin 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H17253  EPDNEW_H17255  EPDNEW_H17256  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38127,155,875 - 7,155,935EPDNEW
RGD ID:6789811
Promoter ID:HG_KWN:14888
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   K562,   Lymphoblastoid,   NB4
Transcripts:NM_014718
Position:
Human AssemblyChrPosition (strand)Source
Build 36127,173,291 - 7,174,372 (+)MPROMDB
RGD ID:6789810
Promoter ID:HG_KWN:14889
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell_12Hour,   K562,   Lymphoblastoid
Transcripts:UC001QSS.1
Position:
Human AssemblyChrPosition (strand)Source
Build 36127,175,371 - 7,176,902 (+)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 12p13.33-11.22(chr12:121055-28415184)x1 copy number loss See cases [RCV000052776] Chr12:121055..28415184 [GRCh38]
Chr12:282465..28568117 [GRCh37]
Chr12:100482..28459384 [NCBI36]
Chr12:12p13.33-11.22
pathogenic
GRCh38/hg38 12p13.31(chr12:6728665-7705620)x1 copy number loss See cases [RCV000052779] Chr12:6728665..7705620 [GRCh38]
Chr12:6837831..7858216 [GRCh37]
Chr12:6708092..7749483 [NCBI36]
Chr12:12p13.31
pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:77187-34380176)x3 copy number gain See cases [RCV000053660] Chr12:77187..34380176 [GRCh38]
Chr12:282465..34533111 [GRCh37]
Chr12:56614..34424378 [NCBI36]
Chr12:12p13.33-11.1
pathogenic
GRCh38/hg38 12p13.33-12.1(chr12:80412-25470329)x3 copy number gain See cases [RCV000053662] Chr12:80412..25470329 [GRCh38]
Chr12:282465..25623263 [GRCh37]
Chr12:59839..25514530 [NCBI36]
Chr12:12p13.33-12.1
pathogenic
GRCh38/hg38 12p13.33-13.31(chr12:121055-7272606)x3 copy number gain See cases [RCV000053663] Chr12:121055..7272606 [GRCh38]
Chr12:282465..7425202 [GRCh37]
Chr12:100482..7316469 [NCBI36]
Chr12:12p13.33-13.31
pathogenic
GRCh38/hg38 12p13.33-13.31(chr12:121255-8361746)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053664]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053664]|See cases [RCV000053664] Chr12:121255..8361746 [GRCh38]
Chr12:282465..8514342 [GRCh37]
Chr12:100682..8405609 [NCBI36]
Chr12:12p13.33-13.31
pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:212976-33926913)x4 copy number gain See cases [RCV000053666] Chr12:212976..33926913 [GRCh38]
Chr12:322142..34079848 [GRCh37]
Chr12:192403..33971115 [NCBI36]
Chr12:12p13.33-11.1
pathogenic
NM_014718.4(CLSTN3):c.599T>C (p.Ile200Thr) single nucleotide variant Autism spectrum disorder [RCV001291196] Chr12:7135810 [GRCh38]
Chr12:7288406 [GRCh37]
Chr12:12p13.31
association
GRCh38/hg38 12p13.33-11.1(chr12:121255-34603274)x3 copy number gain See cases [RCV000136611] Chr12:121255..34603274 [GRCh38]
Chr12:282465..34756209 [GRCh37]
Chr12:100682..34647476 [NCBI36]
Chr12:12p13.33-11.1
pathogenic
GRCh38/hg38 12p13.33-12.3(chr12:2871741-14987348)x3 copy number gain See cases [RCV000137694] Chr12:2871741..14987348 [GRCh38]
Chr12:2980907..15140282 [GRCh37]
Chr12:2851168..15031549 [NCBI36]
Chr12:12p13.33-12.3
pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:121271-34603261)x3 copy number gain See cases [RCV000139052] Chr12:121271..34603261 [GRCh38]
Chr12:282465..34756196 [GRCh37]
Chr12:100698..34647463 [NCBI36]
Chr12:12p13.33-11.1
pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:54427-34608071)x4 copy number gain See cases [RCV000139787] Chr12:54427..34608071 [GRCh38]
Chr12:282465..34761006 [GRCh37]
Chr12:33854..34652273 [NCBI36]
Chr12:12p13.33-11.1
pathogenic
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3 copy number gain See cases [RCV000139555] Chr12:121271..133196807 [GRCh38]
Chr12:282465..133773393 [GRCh37]
Chr12:100698..132283466 [NCBI36]
Chr12:12p13.33-q24.33
pathogenic
GRCh38/hg38 12p13.31(chr12:7055795-7428473)x3 copy number gain See cases [RCV000141432] Chr12:7055795..7428473 [GRCh38]
Chr12:7163099..7581069 [GRCh37]
Chr12:7033360..7472336 [NCBI36]
Chr12:12p13.31
uncertain significance
GRCh38/hg38 12p13.33-12.2(chr12:1258274-20657577)x3 copy number gain See cases [RCV000141905] Chr12:1258274..20657577 [GRCh38]
Chr12:1367440..20810511 [GRCh37]
Chr12:1237701..20701778 [NCBI36]
Chr12:12p13.33-12.2
pathogenic
GRCh38/hg38 12p13.33-11.1(chr12:64620-34682902)x4 copy number gain See cases [RCV000142149] Chr12:64620..34682902 [GRCh38]
Chr12:173786..34835837 [GRCh37]
Chr12:44047..34727104 [NCBI36]
Chr12:12p13.33-11.1
pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:148034-34178799)x4 copy number gain See cases [RCV000240164] Chr12:148034..34178799 [GRCh37]
Chr12:12p13.33-11.1
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:1-133851895)x3 copy number gain See cases [RCV000258805] Chr12:1..133851895 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic|likely pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:89061-34178799)x3 copy number gain See cases [RCV000240487] Chr12:89061..34178799 [GRCh37]
Chr12:12p13.33-11.1
pathogenic
GRCh37/hg19 12p13.33-q11(chr12:173786-37869301)x3 copy number gain See cases [RCV000449191] Chr12:173786..37869301 [GRCh37]
Chr12:12p13.33-q11
pathogenic
GRCh37/hg19 12p13.33-12.1(chr12:173786-25286865)x3 copy number gain See cases [RCV000449287] Chr12:173786..25286865 [GRCh37]
Chr12:12p13.33-12.1
pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34835837)x3 copy number gain See cases [RCV000447551] Chr12:173786..34835837 [GRCh37]
Chr12:12p13.33-11.1
pathogenic
GRCh37/hg19 12p13.33-12.2(chr12:173786-20026080)x3 copy number gain See cases [RCV000446050] Chr12:173786..20026080 [GRCh37]
Chr12:12p13.33-12.2
pathogenic
GRCh37/hg19 12p13.33-13.31(chr12:173786-8257049)x3 copy number gain See cases [RCV000446749] Chr12:173786..8257049 [GRCh37]
Chr12:12p13.33-13.31
pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:189578-34756150) copy number gain See cases [RCV000446017] Chr12:189578..34756150 [GRCh37]
Chr12:12p13.33-11.1
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902)x3 copy number gain See cases [RCV000510482] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:565369-34835837)x3 copy number gain See cases [RCV000511580] Chr12:565369..34835837 [GRCh37]
Chr12:12p13.33-11.1
likely pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902) copy number gain See cases [RCV000511643] Chr12:173787..133777902 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
GRCh37/hg19 12p13.33-13.2(chr12:173786-11677456)x3 copy number gain See cases [RCV000510853] Chr12:173786..11677456 [GRCh37]
Chr12:12p13.33-13.2
pathogenic
GRCh37/hg19 12p13.33-11.22(chr12:173786-28219229)x3 copy number gain See cases [RCV000510961] Chr12:173786..28219229 [GRCh37]
Chr12:12p13.33-11.22
pathogenic
GRCh37/hg19 12p13.33-q11(chr12:173786-37869107)x3 copy number gain not provided [RCV000683480] Chr12:173786..37869107 [GRCh37]
Chr12:12p13.33-q11
pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34835837)x2,3 copy number gain not provided [RCV000683478] Chr12:173786..34835837 [GRCh37]
Chr12:12p13.33-11.1
pathogenic
GRCh37/hg19 12p13.33-11.1(chr12:173786-34835837)x3 copy number gain not provided [RCV000683479] Chr12:173786..34835837 [GRCh37]
Chr12:12p13.33-11.1
pathogenic
GRCh37/hg19 12p13.33-13.31(chr12:191242-8122785)x3 copy number gain not provided [RCV000683477] Chr12:191242..8122785 [GRCh37]
Chr12:12p13.33-13.31
pathogenic
NC_000012.12:g.(1_3750000)_(5250000_9000000)del deletion Hyperphosphatemic familial tumoral calcinosis 1 [RCV000758697] Chr12:3750000..5250000 [GRCh38]
Chr12:12p13.33-13.31
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:191619-133777645)x3 copy number gain not provided [RCV000750246] Chr12:191619..133777645 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:621220-133779118)x3 copy number gain not provided [RCV000750253] Chr12:621220..133779118 [GRCh37]
Chr12:12p13.33-q24.33
pathogenic
GRCh37/hg19 12p13.33-11.21(chr12:191619-31733044)x3 copy number gain not provided [RCV000750245] Chr12:191619..31733044 [GRCh37]
Chr12:12p13.33-11.21
pathogenic
GRCh37/hg19 12p13.31(chr12:6911437-9381254)x3 copy number gain not provided [RCV000750277] Chr12:6911437..9381254 [GRCh37]
Chr12:12p13.31
uncertain significance
GRCh37/hg19 12p13.33-q11(chr12:274676-37869301)x4 copy number gain not provided [RCV001006470] Chr12:274676..37869301 [GRCh37]
Chr12:12p13.33-q11
pathogenic
GRCh37/hg19 12p13.33-12.3(chr12:189216-15001420) copy number gain not provided [RCV000767817] Chr12:189216..15001420 [GRCh37]
Chr12:12p13.33-12.3
pathogenic
GRCh37/hg19 12p13.33-13.31(chr12:237588-8278292) copy number gain not provided [RCV000767818] Chr12:237588..8278292 [GRCh37]
Chr12:12p13.33-13.31
pathogenic
GRCh37/hg19 12p13.33-13.31(chr12:189216-8185497) copy number gain not provided [RCV000767819] Chr12:189216..8185497 [GRCh37]
Chr12:12p13.33-13.31
pathogenic
NC_000012.11:g.(?_6945914)_(9027627_?)dup duplication Temtamy syndrome [RCV000816630] Chr12:6945914..9027627 [GRCh37]
Chr12:12p13.31
uncertain significance
GRCh37/hg19 12p13.33-11.1(chr12:173786-34496628)x3 copy number gain not provided [RCV000847209] Chr12:173786..34496628 [GRCh37]
Chr12:12p13.33-11.1
pathogenic
GRCh37/hg19 12p13.33-13.31(chr12:173786-8393815)x3 copy number gain not provided [RCV000846343] Chr12:173786..8393815 [GRCh37]
Chr12:12p13.33-13.31
pathogenic
GRCh37/hg19 12p13.31(chr12:7162134-7605102)x3 copy number gain not provided [RCV000849455] Chr12:7162134..7605102 [GRCh37]
Chr12:12p13.31
uncertain significance
GRCh37/hg19 12p13.33-13.31(chr12:189145-7730395)x3 copy number gain not provided [RCV001537906] Chr12:189145..7730395 [GRCh37]
Chr12:12p13.33-13.31
pathogenic
NC_000012.11:g.(?_6945914)_(8248706_?)dup duplication Temtamy syndrome [RCV001031096] Chr12:6945914..8248706 [GRCh37]
Chr12:12p13.31
uncertain significance
NC_000012.11:g.(?_6438458)_(7362839_?)dup duplication Peroxisome biogenesis disorder 2B [RCV001031288] Chr12:6438458..7362839 [GRCh37]
Chr12:12p13.31
uncertain significance
NC_000012.11:g.(?_6945914)_(9027627_?)dup duplication Early infantile epileptic encephalopathy 21 [RCV001325295]|Klippel-Feil syndrome 3, autosomal dominant [RCV001301079]|Temtamy syndrome [RCV000816630] Chr12:6945914..9027627 [GRCh37]
Chr12:12p13.31
uncertain significance
NC_000012.11:g.(?_6438478)_(7362819_?)dup duplication Temtamy syndrome [RCV001365174] Chr12:6438478..7362819 [GRCh37]
Chr12:12p13.31
uncertain significance

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:18371 AgrOrtholog
COSMIC CLSTN3 COSMIC
Ensembl Genes ENSG00000139182 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSG00000288427 UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000266546 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSP00000442612 UniProtKB/TrEMBL
  ENSP00000442801 UniProtKB/TrEMBL
  ENSP00000443468 UniProtKB/TrEMBL
  ENSP00000443490 UniProtKB/TrEMBL
  ENSP00000443959 UniProtKB/TrEMBL
  ENSP00000496782 UniProtKB/TrEMBL
  ENSP00000497486 UniProtKB/TrEMBL
  ENSP00000500510 UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000266546 ENTREZGENE, UniProtKB/Swiss-Prot
  ENST00000331148 UniProtKB/TrEMBL
  ENST00000534830 UniProtKB/TrEMBL
  ENST00000535313 UniProtKB/TrEMBL
  ENST00000535452 UniProtKB/TrEMBL
  ENST00000537408 ENTREZGENE
  ENST00000539982 UniProtKB/TrEMBL
  ENST00000541953 UniProtKB/TrEMBL
  ENST00000545663 UniProtKB/TrEMBL
  ENST00000672495 UniProtKB/Swiss-Prot
GTEx ENSG00000139182 GTEx
  ENSG00000288427 GTEx
HGNC ID HGNC:18371 ENTREZGENE
Human Proteome Map CLSTN3 Human Proteome Map
InterPro Cadherin-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cadherin-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Calsyntenin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ConA-like_dom_sf UniProtKB/Swiss-Prot
KEGG Report hsa:9746 UniProtKB/Swiss-Prot
NCBI Gene 9746 ENTREZGENE
OMIM 611324 OMIM
PANTHER PTHR14139 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/Swiss-Prot
PharmGKB PA38320 PharmGKB
PRINTS CADHERIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CADHERIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00112 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF49313 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49899 UniProtKB/Swiss-Prot
UniProt A0A3B3IRF8_HUMAN UniProtKB/TrEMBL
  A0A3B3ISW0_HUMAN UniProtKB/TrEMBL
  CSTN3_HUMAN UniProtKB/Swiss-Prot
  F5H172_HUMAN UniProtKB/TrEMBL
  F5H5C6_HUMAN UniProtKB/TrEMBL
  F5H5D7_HUMAN UniProtKB/TrEMBL
  F5H746_HUMAN UniProtKB/TrEMBL
  F5H7C7_HUMAN UniProtKB/TrEMBL
  Q8IUW6_HUMAN UniProtKB/TrEMBL
  Q9BQT9 ENTREZGENE
UniProt Secondary D3DUT6 UniProtKB/Swiss-Prot
  O94831 UniProtKB/Swiss-Prot
  Q2T9J5 UniProtKB/Swiss-Prot
  Q5UE57 UniProtKB/Swiss-Prot