VAMP4 (vesicle associated membrane protein 4) - Rat Genome Database

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Gene: VAMP4 (vesicle associated membrane protein 4) Homo sapiens
Analyze
Symbol: VAMP4
Name: vesicle associated membrane protein 4
RGD ID: 1320258
HGNC Page HGNC:12645
Description: Involved in SNARE complex assembly and endocytic recycling. Located in Golgi apparatus and cell surface.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: VAMP-4; VAMP24; VAMP4/TAF3 fusion; vesicle-associated membrane protein 4
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
GRCh381171,700,160 - 171,742,065 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1171,700,160 - 171,742,074 (-)EnsemblGRCh38hg38GRCh38
GRCh371171,669,300 - 171,711,205 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361169,938,783 - 169,977,837 (-)NCBINCBI36Build 36hg18NCBI36
Celera1144,778,698 - 144,820,780 (-)NCBICelera
Cytogenetic Map1q24.3NCBI
HuRef1142,893,046 - 142,935,123 (-)NCBIHuRef
CHM1_11173,091,387 - 173,133,527 (-)NCBICHM1_1
T2T-CHM13v2.01171,056,627 - 171,098,537 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8619474   PMID:9110174   PMID:9553086   PMID:10359608   PMID:10839363   PMID:11598115   PMID:11839770   PMID:12477932   PMID:12682051   PMID:14608369   PMID:14702039   PMID:15345747  
PMID:15489334   PMID:15896658   PMID:16189514   PMID:16344560   PMID:17081983   PMID:19557002   PMID:20685960   PMID:21151919   PMID:21805468   PMID:21873635   PMID:22406549   PMID:23585472  
PMID:23677696   PMID:23741335   PMID:23798538   PMID:24623722   PMID:25416956   PMID:25419848   PMID:26186194   PMID:26359495   PMID:26496610   PMID:26638075   PMID:27791468   PMID:28514442  
PMID:28626000   PMID:29568061   PMID:29997244   PMID:30021884   PMID:30194290   PMID:30833792   PMID:31391242   PMID:32296183   PMID:32393512   PMID:32873436   PMID:33845483   PMID:33961781  
PMID:34079125   PMID:34369648   PMID:34597346   PMID:34672954   PMID:35156780   PMID:35271311   PMID:36053215   PMID:37774976   PMID:38117590  


Genomics

Comparative Map Data
VAMP4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381171,700,160 - 171,742,065 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1171,700,160 - 171,742,074 (-)EnsemblGRCh38hg38GRCh38
GRCh371171,669,300 - 171,711,205 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361169,938,783 - 169,977,837 (-)NCBINCBI36Build 36hg18NCBI36
Celera1144,778,698 - 144,820,780 (-)NCBICelera
Cytogenetic Map1q24.3NCBI
HuRef1142,893,046 - 142,935,123 (-)NCBIHuRef
CHM1_11173,091,387 - 173,133,527 (-)NCBICHM1_1
T2T-CHM13v2.01171,056,627 - 171,098,537 (-)NCBIT2T-CHM13v2.0
Vamp4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391162,398,084 - 162,426,651 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1162,398,084 - 162,426,653 (+)EnsemblGRCm39 Ensembl
GRCm381162,570,515 - 162,599,082 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1162,570,515 - 162,599,084 (+)EnsemblGRCm38mm10GRCm38
MGSCv371164,500,959 - 164,529,209 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361164,407,503 - 164,435,753 (+)NCBIMGSCv36mm8
Celera1165,015,226 - 165,045,414 (+)NCBICelera
Cytogenetic Map1H2.1NCBI
cM Map170.29NCBI
Vamp4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81377,453,135 - 77,475,909 (+)NCBIGRCr8
mRatBN7.21374,919,872 - 74,942,791 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1374,919,880 - 74,933,686 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1377,495,346 - 77,520,525 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01378,802,728 - 78,825,319 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01376,062,597 - 76,085,190 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01380,460,699 - 80,483,597 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1380,460,694 - 80,483,600 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01385,352,779 - 85,375,559 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41378,247,189 - 78,269,770 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11378,261,180 - 78,280,664 (+)NCBI
Celera1374,670,256 - 74,692,771 (+)NCBICelera
Cytogenetic Map13q22NCBI
Vamp4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540612,223,736 - 12,260,317 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540612,223,736 - 12,260,506 (-)NCBIChiLan1.0ChiLan1.0
VAMP4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2178,013,280 - 78,058,507 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1177,687,698 - 77,732,898 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01147,192,001 - 147,233,945 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11150,903,134 - 150,944,815 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1150,903,134 - 150,944,815 (-)Ensemblpanpan1.1panPan2
VAMP4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1727,278,200 - 27,303,499 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl727,278,231 - 27,302,225 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha726,797,085 - 26,827,670 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0727,078,744 - 27,107,216 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl727,051,313 - 27,107,216 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1726,900,757 - 26,958,730 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0726,935,355 - 26,993,045 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0727,207,418 - 27,232,436 (+)NCBIUU_Cfam_GSD_1.0
Vamp4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934497,634,092 - 97,669,945 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648115,480,879 - 15,516,945 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493648115,480,865 - 15,515,851 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VAMP4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9114,138,330 - 114,174,979 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19114,138,350 - 114,174,996 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29125,606,175 - 125,638,921 (-)NCBISscrofa10.2Sscrofa10.2susScr3
VAMP4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12557,381,143 - 57,421,886 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2557,384,757 - 57,421,893 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605559,006,290 - 59,051,034 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vamp4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247719,986,835 - 10,034,112 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in VAMP4
5 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1q23.1-25.1(chr1:157747246-176021247)x3 copy number gain See cases [RCV000051854] Chr1:157747246..176021247 [GRCh38]
Chr1:157717036..175990383 [GRCh37]
Chr1:155983660..174257006 [NCBI36]
Chr1:1q23.1-25.1		 pathogenic
GRCh38/hg38 1q23.3-25.2(chr1:164922655-180061589)x3 copy number gain See cases [RCV000051856] Chr1:164922655..180061589 [GRCh38]
Chr1:164891892..180030724 [GRCh37]
Chr1:163158516..178297347 [NCBI36]
Chr1:1q23.3-25.2		 pathogenic
GRCh38/hg38 1q24.2-25.1(chr1:168314822-175299299)x1 copy number loss See cases [RCV000053918] Chr1:168314822..175299299 [GRCh38]
Chr1:168284060..175268435 [GRCh37]
Chr1:166550684..173535058 [NCBI36]
Chr1:1q24.2-25.1		 pathogenic
GRCh38/hg38 1q23.3-25.1(chr1:161740907-173965154)x1 copy number loss See cases [RCV000053914] Chr1:161740907..173965154 [GRCh38]
Chr1:161710697..173934292 [GRCh37]
Chr1:159977321..172200915 [NCBI36]
Chr1:1q23.3-25.1		 pathogenic
GRCh38/hg38 1q24.1-25.1(chr1:166762832-175327423)x1 copy number loss See cases [RCV000053917] Chr1:166762832..175327423 [GRCh38]
Chr1:166732069..175296559 [GRCh37]
Chr1:164998693..173563182 [NCBI36]
Chr1:1q24.1-25.1		 pathogenic
GRCh38/hg38 1q24.3-31.1(chr1:171039975-186875957)x3 copy number gain See cases [RCV000134876] Chr1:171039975..186875957 [GRCh38]
Chr1:171009116..186845089 [GRCh37]
Chr1:169275740..185111712 [NCBI36]
Chr1:1q24.3-31.1		 pathogenic
GRCh38/hg38 1q24.2-25.2(chr1:169218236-178075834)x1 copy number loss See cases [RCV000137128] Chr1:169218236..178075834 [GRCh38]
Chr1:169187474..178044969 [GRCh37]
Chr1:167454098..176311592 [NCBI36]
Chr1:1q24.2-25.2		 pathogenic
GRCh38/hg38 1q24.3-31.2(chr1:170929720-191065409)x1 copy number loss See cases [RCV000142369] Chr1:170929720..191065409 [GRCh38]
Chr1:170898861..191034539 [GRCh37]
Chr1:169165485..189301162 [NCBI36]
Chr1:1q24.3-31.2		 pathogenic
GRCh38/hg38 1q23.3-25.1(chr1:163382523-175877022)x1 copy number loss See cases [RCV000143292] Chr1:163382523..175877022 [GRCh38]
Chr1:163352313..175846158 [GRCh37]
Chr1:161618937..174112781 [NCBI36]
Chr1:1q23.3-25.1		 pathogenic
GRCh38/hg38 1q24.2-31.1(chr1:170036068-187555148)x1 copy number loss See cases [RCV000143688] Chr1:170036068..187555148 [GRCh38]
Chr1:170005209..187524280 [GRCh37]
Chr1:168271833..185790903 [NCBI36]
Chr1:1q24.2-31.1		 pathogenic
GRCh38/hg38 1q21.2-25.2(chr1:149854269-180267197)x3 copy number gain See cases [RCV000143515] Chr1:149854269..180267197 [GRCh38]
Chr1:149825831..180236332 [GRCh37]
Chr1:148092455..178502955 [NCBI36]
Chr1:1q21.2-25.2		 pathogenic
GRCh37/hg19 1q23.2-25.1(chr1:160369890-175796325) copy number loss not provided [RCV000767779] Chr1:160369890..175796325 [GRCh37]
Chr1:1q23.2-25.1		 pathogenic
GRCh37/hg19 1q23.3-25.3(chr1:161676893-184071723)x1 copy number loss See cases [RCV000447098] Chr1:161676893..184071723 [GRCh37]
Chr1:1q23.3-25.3		 pathogenic
GRCh37/hg19 1q24.3(chr1:171698731-171765591)x1 copy number loss See cases [RCV000446671] Chr1:171698731..171765591 [GRCh37]
Chr1:1q24.3		 uncertain significance
GRCh37/hg19 1q24.2-25.3(chr1:169873155-181823980)x1 copy number loss See cases [RCV000447593] Chr1:169873155..181823980 [GRCh37]
Chr1:1q24.2-25.3		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
Single allele deletion 1q24q25 microdeletion syndrome [RCV000754969] Chr1:169095250..175778910 [GRCh37]
Chr1:1q24.2-25.1		 pathogenic
GRCh37/hg19 1q23.2-25.2(chr1:159815642-177026983)x1 copy number loss not provided [RCV000736717] Chr1:159815642..177026983 [GRCh37]
Chr1:1q23.2-25.2		 pathogenic
GRCh37/hg19 1q24.2-25.3(chr1:169423492-180367623) copy number gain not provided [RCV000767621] Chr1:169423492..180367623 [GRCh37]
Chr1:1q24.2-25.3		 pathogenic
GRCh37/hg19 1q24.2-25.1(chr1:167430471-174635618)x1 copy number loss not provided [RCV001005149] Chr1:167430471..174635618 [GRCh37]
Chr1:1q24.2-25.1		 pathogenic
NC_000001.10:g.(?_130980840)_(248900000_?)dup duplication Gastrointestinal stromal tumor [RCV001300221]|Parathyroid carcinoma [RCV001341077] Chr1:130980840..248900000 [GRCh37]
Chr1:1q12-44		 uncertain significance
NC_000001.10:g.(?_171605065)_(173962123_?)del deletion Autoimmune lymphoproliferative syndrome type 1 [RCV001947302]|not provided [RCV001947303] Chr1:171605065..173962123 [GRCh37]
Chr1:1q24.3-25.1		 pathogenic|uncertain significance|no classifications from unflagged records
GRCh37/hg19 1q24.2-24.3(chr1:167391422-171843613) copy number loss not specified [RCV002053691] Chr1:167391422..171843613 [GRCh37]
Chr1:1q24.2-24.3		 pathogenic
GRCh37/hg19 1q24.2-25.3(chr1:169873155-181823980) copy number loss not specified [RCV002053713] Chr1:169873155..181823980 [GRCh37]
Chr1:1q24.2-25.3		 pathogenic
NC_000001.10:g.(?_171605065)_(173962123_?)dup duplication Autoimmune lymphoproliferative syndrome type 1 [RCV001939952] Chr1:171605065..173962123 [GRCh37]
Chr1:1q24.3-25.1		 uncertain significance
GRCh37/hg19 1q24.3(chr1:171649657-172399870)x1 copy number loss See cases [RCV002287554] Chr1:171649657..172399870 [GRCh37]
Chr1:1q24.3		 uncertain significance
GRCh37/hg19 1q24.3(chr1:171186446-171907499)x3 copy number gain not provided [RCV002475832] Chr1:171186446..171907499 [GRCh37]
Chr1:1q24.3		 uncertain significance
NM_003762.5(VAMP4):c.358A>G (p.Met120Val) single nucleotide variant Inborn genetic diseases [RCV002935021] Chr1:171706406 [GRCh38]
Chr1:171675546 [GRCh37]
Chr1:1q24.3		 uncertain significance
NM_003762.5(VAMP4):c.304T>G (p.Ser102Ala) single nucleotide variant Inborn genetic diseases [RCV002672705] Chr1:171709706 [GRCh38]
Chr1:171678846 [GRCh37]
Chr1:1q24.3		 uncertain significance
NM_003762.5(VAMP4):c.404T>C (p.Ile135Thr) single nucleotide variant Inborn genetic diseases [RCV003348051] Chr1:171704528 [GRCh38]
Chr1:171673668 [GRCh37]
Chr1:1q24.3		 uncertain significance
GRCh37/hg19 1q23.3-25.1(chr1:164571371-175708060)x1 copy number loss not provided [RCV003483966] Chr1:164571371..175708060 [GRCh37]
Chr1:1q23.3-25.1		 pathogenic
GRCh37/hg19 1q24.2-31.1(chr1:167994071-187711459)x1 copy number loss not specified [RCV003987250] Chr1:167994071..187711459 [GRCh37]
Chr1:1q24.2-31.1		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2724
Count of miRNA genes:806
Interacting mature miRNAs:950
Transcripts:ENST00000236192, ENST00000367740, ENST00000415773, ENST00000474047, ENST00000482519
Prediction methods: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.

Markers in Region
AL033823  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371171,712,383 - 171,712,465UniSTSGRCh37
Build 361169,979,006 - 169,979,088RGDNCBI36
Celera1144,821,784 - 144,821,866RGD
Cytogenetic Map1q24-q25UniSTS
HuRef1142,936,127 - 142,936,209UniSTS
AL034156  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371171,669,773 - 171,669,932UniSTSGRCh37
Build 361169,936,396 - 169,936,555RGDNCBI36
Celera1144,779,175 - 144,779,334RGD
Cytogenetic Map1q24-q25UniSTS
HuRef1142,893,523 - 142,893,682UniSTS
G42281  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371171,706,536 - 171,706,677UniSTSGRCh37
Build 361169,973,159 - 169,973,300RGDNCBI36
Celera1144,815,937 - 144,816,078RGD
Cytogenetic Map1q24-q25UniSTS
HuRef1142,930,280 - 142,930,421UniSTS
G42285  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371171,681,357 - 171,681,561UniSTSGRCh37
Build 361169,947,980 - 169,948,184RGDNCBI36
Celera1144,790,757 - 144,790,961RGD
Cytogenetic Map1q24-q25UniSTS
HuRef1142,905,105 - 142,905,309UniSTS
SHGC-82902  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371171,710,292 - 171,710,580UniSTSGRCh37
Build 361169,976,915 - 169,977,203RGDNCBI36
Celera1144,819,693 - 144,819,981RGD
Cytogenetic Map1q24-q25UniSTS
HuRef1142,934,036 - 142,934,324UniSTS
TNG Radiation Hybrid Map161427.0UniSTS
RH102530  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371171,673,151 - 171,673,305UniSTSGRCh37
Build 361169,939,774 - 169,939,928RGDNCBI36
Celera1144,782,551 - 144,782,705RGD
Cytogenetic Map1q24-q25UniSTS
HuRef1142,896,899 - 142,897,053UniSTS
GeneMap99-GB4 RH Map1621.18UniSTS
SHGC-144585  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371171,682,785 - 171,683,110UniSTSGRCh37
Build 361169,949,408 - 169,949,733RGDNCBI36
Celera1144,792,185 - 144,792,510RGD
Cytogenetic Map1q24-q25UniSTS
HuRef1142,906,533 - 142,906,858UniSTS
TNG Radiation Hybrid Map161453.0UniSTS
A009C32  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371171,670,874 - 171,670,974UniSTSGRCh37
Build 361169,937,497 - 169,937,597RGDNCBI36
Celera1144,780,276 - 144,780,376RGD
Cytogenetic Map1q24-q25UniSTS
HuRef1142,894,624 - 142,894,724UniSTS
GeneMap99-GB4 RH Map1623.4UniSTS
D1S2532  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371171,669,372 - 171,669,450UniSTSGRCh37
Build 361169,935,995 - 169,936,073RGDNCBI36
Celera1144,778,774 - 144,778,852RGD
Cytogenetic Map1q24-q25UniSTS
HuRef1142,893,122 - 142,893,200UniSTS
TNG Radiation Hybrid Map161466.0UniSTS
GeneMap99-GB4 RH Map1619.31UniSTS
D1S2351  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371171,669,327 - 171,669,530UniSTSGRCh37
Build 361169,935,950 - 169,936,153RGDNCBI36
Celera1144,778,729 - 144,778,932RGD
Cytogenetic Map1q24-q25UniSTS
HuRef1142,893,077 - 142,893,280UniSTS
GeneMap99-GB4 RH Map1621.18UniSTS
GeneMap99-GB4 RH Map1623.4UniSTS
Whitehead-RH Map1771.6UniSTS
Whitehead-YAC Contig Map1 UniSTS
D1S3031  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371171,669,327 - 171,669,507UniSTSGRCh37
Build 361169,935,950 - 169,936,130RGDNCBI36
Celera1144,778,729 - 144,778,909RGD
Cytogenetic Map1q24-q25UniSTS
HuRef1142,893,077 - 142,893,257UniSTS
GeneMap99-GB4 RH Map1621.18UniSTS
Whitehead-RH Map1771.6UniSTS
Whitehead-YAC Contig Map1 UniSTS
SHGC-75917  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371171,670,531 - 171,670,659UniSTSGRCh37
Build 361169,937,154 - 169,937,282RGDNCBI36
Celera1144,779,933 - 144,780,061RGD
Cytogenetic Map1q24-q25UniSTS
HuRef1142,894,281 - 142,894,409UniSTS
TNG Radiation Hybrid Map161479.0UniSTS
GeneMap99-GB4 RH Map1623.4UniSTS
G32422  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371171,670,874 - 171,670,974UniSTSGRCh37
Celera1144,780,276 - 144,780,376UniSTS
Cytogenetic Map1q24-q25UniSTS
HuRef1142,894,624 - 142,894,724UniSTS


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 1784 1385 1212 176 765 62 3259 936 2805 189 1238 1492 117 996 1914 1
Low 655 1601 514 448 1181 403 1098 1261 928 230 222 121 57 1 208 874 4 2
Below cutoff 5 5 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001185127 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_003762 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_033704 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017002713 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047433375 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054339395 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AF044310 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF052100 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK056124 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK123624 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK290441 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL035296 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC005974 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC007019 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC031264 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471067 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR457011 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  DB167275 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY966279 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  KY966300 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Z98751 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000236192   ⟹   ENSP00000236192
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1171,700,160 - 171,742,065 (-)Ensembl
RefSeq Acc Id: ENST00000367740   ⟹   ENSP00000356714
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1171,703,950 - 171,742,074 (-)Ensembl
RefSeq Acc Id: ENST00000474047   ⟹   ENSP00000435933
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1171,701,092 - 171,742,060 (-)Ensembl
RefSeq Acc Id: ENST00000482519
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1171,704,505 - 171,742,065 (-)Ensembl
RefSeq Acc Id: NM_001185127   ⟹   NP_001172056
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381171,700,160 - 171,742,065 (-)NCBI
GRCh371171,669,296 - 171,711,379 (-)RGD
Celera1144,778,698 - 144,820,780 (-)RGD
HuRef1142,893,046 - 142,935,123 (-)ENTREZGENE
CHM1_11173,091,387 - 173,133,527 (-)NCBI
T2T-CHM13v2.01171,056,627 - 171,098,537 (-)NCBI
Sequence:
RefSeq Acc Id: NM_003762   ⟹   NP_003753
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381171,700,160 - 171,742,065 (-)NCBI
GRCh371171,669,296 - 171,711,379 (-)RGD
Build 361169,938,783 - 169,977,837 (-)NCBI Archive
Celera1144,778,698 - 144,820,780 (-)RGD
HuRef1142,893,046 - 142,935,123 (-)ENTREZGENE
CHM1_11173,091,387 - 173,133,527 (-)NCBI
T2T-CHM13v2.01171,056,627 - 171,098,537 (-)NCBI
Sequence:
RefSeq Acc Id: NR_033704
RefSeq Status: REVIEWED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381171,700,160 - 171,742,065 (-)NCBI
GRCh371171,669,296 - 171,711,379 (-)RGD
Celera1144,778,698 - 144,820,780 (-)RGD
HuRef1142,893,046 - 142,935,123 (-)ENTREZGENE
CHM1_11173,091,387 - 173,133,527 (-)NCBI
T2T-CHM13v2.01171,056,627 - 171,098,537 (-)NCBI
Sequence:
RefSeq Acc Id: XM_047433375   ⟹   XP_047289331
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381171,709,698 - 171,742,065 (-)NCBI
RefSeq Acc Id: XM_054339395   ⟹   XP_054195370
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01171,066,169 - 171,098,537 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_003753   ⟸   NM_003762
- Peptide Label: isoform 1
- UniProtKB: Q96J20 (UniProtKB/Swiss-Prot),   Q96IY9 (UniProtKB/Swiss-Prot),   A2IDD8 (UniProtKB/Swiss-Prot),   Q9UEL7 (UniProtKB/Swiss-Prot),   O75379 (UniProtKB/Swiss-Prot),   Q6IAZ3 (UniProtKB/TrEMBL),   A0A024R8Z6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001172056   ⟸   NM_001185127
- Peptide Label: isoform 2
- UniProtKB: O75379 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000356714   ⟸   ENST00000367740
RefSeq Acc Id: ENSP00000236192   ⟸   ENST00000236192
RefSeq Acc Id: ENSP00000435933   ⟸   ENST00000474047
RefSeq Acc Id: XP_047289331   ⟸   XM_047433375
- Peptide Label: isoform X1
RefSeq Acc Id: XP_054195370   ⟸   XM_054339395
- Peptide Label: isoform X1
Protein Domains
v-SNARE coiled-coil homology

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O75379-F1-model_v2 AlphaFold O75379 1-141 view protein structure

Promoters
RGD ID:6814460
Promoter ID:HG_XEF:597
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562,   Lymphoblastoid
Transcripts:NM_001076438
Position:
Human AssemblyChrPosition (strand)Source
Build 361169,976,971 - 169,977,471 (-)MPROMDB
RGD ID:6787204
Promoter ID:HG_KWN:6185
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000236192,   OTTHUMT00000084177,   UC001GHW.1,   UC001GHY.1
Position:
Human AssemblyChrPosition (strand)Source
Build 361169,977,794 - 169,978,294 (-)MPROMDB
RGD ID:6858116
Promoter ID:EPDNEW_H2222
Type:initiation region
Name:VAMP4_1
Description:vesicle associated membrane protein 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H2223  EPDNEW_H2224  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381171,742,065 - 171,742,125EPDNEW
RGD ID:6858118
Promoter ID:EPDNEW_H2223
Type:initiation region
Name:VAMP4_3
Description:vesicle associated membrane protein 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H2222  EPDNEW_H2224  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381171,742,183 - 171,742,243EPDNEW
RGD ID:6858120
Promoter ID:EPDNEW_H2224
Type:multiple initiation site
Name:VAMP4_2
Description:vesicle associated membrane protein 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H2222  EPDNEW_H2223  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh381171,743,206 - 171,743,266EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:12645 AgrOrtholog
COSMIC VAMP4 COSMIC
Ensembl Genes ENSG00000117533 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000236192 ENTREZGENE
  ENST00000236192.12 UniProtKB/Swiss-Prot
  ENST00000367740 ENTREZGENE
  ENST00000367740.2 UniProtKB/Swiss-Prot
  ENST00000474047.5 UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.5.110 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000117533 GTEx
HGNC ID HGNC:12645 ENTREZGENE
Human Proteome Map VAMP4 Human Proteome Map
InterPro Synaptobrevin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  V_SNARE_CC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VAMP4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:8674 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 8674 ENTREZGENE
OMIM 606909 OMIM
PANTHER PTHR46897 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VESICLE-ASSOCIATED MEMBRANE PROTEIN 4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Synaptobrevin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA37269 PharmGKB
PRINTS SYNAPTOBREVN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE SYNAPTOBREVIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  V_SNARE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SNARE fusion complex UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A024R8Z6 ENTREZGENE
  A2IDD8 ENTREZGENE
  O75379 ENTREZGENE
  Q6IAZ3 ENTREZGENE, UniProtKB/TrEMBL
  Q96IY9 ENTREZGENE
  Q96J20 ENTREZGENE
  Q9UEL7 ENTREZGENE
  VAMP4_HUMAN UniProtKB/Swiss-Prot
UniProt Secondary A0A024R8Z6 UniProtKB/TrEMBL
  A2IDD8 UniProtKB/Swiss-Prot
  Q96IY9 UniProtKB/Swiss-Prot
  Q96J20 UniProtKB/Swiss-Prot
  Q9UEL7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-10 VAMP4  vesicle associated membrane protein 4  VAMP4  vesicle-associated membrane protein 4  Symbol and/or name change 5135510 APPROVED