VPS54 (VPS54 subunit of GARP complex) - Rat Genome Database

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Gene: VPS54 (VPS54 subunit of GARP complex) Homo sapiens
Analyze
Symbol: VPS54
Name: VPS54 subunit of GARP complex
RGD ID: 1350552
HGNC Page HGNC:18652
Description: Predicted to enable syntaxin binding activity. Acts upstream of or within lysosomal transport and retrograde transport, endosome to Golgi. Located in nucleoplasm; perinuclear region of cytoplasm; and trans-Golgi network. Part of GARP complex.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: HCC8; hepatocellular carcinoma protein 8; hVps54L; PPP1R164; SLP-8p; tumor antigen HOM-HCC-8; tumor antigen SLP-8p; vacuolar protein sorting 54 (yeast); vacuolar protein sorting 54 homolog; vacuolar protein sorting-associated protein 54; VPS54 GARP complex subunit; VPS54, GARP complex subunit; VPS54L; WR
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38263,892,150 - 64,019,428 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl263,892,146 - 64,019,428 (-)EnsemblGRCh38hg38GRCh38
GRCh37264,119,284 - 64,246,562 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36263,973,171 - 64,099,718 (-)NCBINCBI36Build 36hg18NCBI36
Build 34264,031,317 - 64,157,865NCBI
Celera263,964,934 - 64,091,495 (-)NCBICelera
Cytogenetic Map2p15-p14NCBI
HuRef263,859,380 - 63,986,062 (-)NCBIHuRef
CHM1_1264,049,942 - 64,176,502 (-)NCBICHM1_1
T2T-CHM13v2.0263,899,706 - 64,027,065 (-)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

Biological Process
apoptotic DNA fragmentation  (IEA)
astrocyte differentiation  (IEA)
cellular response to progesterone stimulus  (IEA)
gene expression  (IEA)
Golgi to vacuole transport  (IBA,IEA)
homeostasis of number of cells  (IEA)
homeostasis of number of cells within a tissue  (IEA,ISO)
in utero embryonic development  (IEA)
intracellular calcium ion homeostasis  (IEA)
L-glutamate import  (IEA)
limb development  (IEA)
limb morphogenesis  (IEA)
lysosomal transport  (IMP)
microglia differentiation  (IEA)
mitochondrion organization  (IEA)
motor behavior  (IEA)
motor neuron apoptotic process  (IEA)
musculoskeletal movement  (IEA,ISO)
negative regulation of motor neuron apoptotic process  (IEA)
neural tissue regeneration  (IEA)
neurofilament cytoskeleton organization  (IEA,ISO)
neuroinflammatory response  (IEA)
neuromuscular synaptic transmission  (IEA)
neuron apoptotic process  (IEA)
neuron projection morphogenesis  (IEA)
post-embryonic forelimb morphogenesis  (IEA)
protein localization  (IEA)
protein localization to cell surface  (IEA)
protein targeting to ER  (IEA)
protein targeting to lysosome  (IEA)
protein targeting to vacuole  (IEA)
protein transport  (IEA)
regulation of growth  (IEA,ISO)
respiratory electron transport chain  (IEA)
response to antibiotic  (IEA)
response to calcium ion  (IEA)
retrograde transport, endosome to Golgi  (IBA,IEA,IMP,NAS)
skeletal muscle tissue development  (IEA)
skeletal muscle tissue growth  (IEA)
spermatid differentiation  (IEA)
sphingolipid catabolic process  (IEA)
striated muscle contraction  (IEA)
synaptic transmission, GABAergic  (IEA)
synaptic transmission, glutamatergic  (IEA)
thrombin-activated receptor signaling pathway  (IEA)
ubiquitin recycling  (IEA)
vacuole organization  (IEA)
vesicle-mediated cholesterol transport  (IEA)

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
Tooth agenesis  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. GOAs Human GO annotations GOA_HUMAN data from the GO Consortium
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Identification, characterization and cytogenetic mapping of a yeast Vps54 homolog in rat and mouse. Walter L, etal., Gene 2002 Feb 20;285(1-2):213-20.
Additional References at PubMed
PMID:3172165   PMID:12174196   PMID:12477932   PMID:14702039   PMID:15489334   PMID:15878329   PMID:18367545   PMID:18574757   PMID:19389623   PMID:19620288   PMID:20379614   PMID:20615984  
PMID:20685960   PMID:21087364   PMID:21873635   PMID:25187353   PMID:25795912   PMID:25799061   PMID:26186194   PMID:26472760   PMID:26496610   PMID:27440922   PMID:28514442   PMID:28611215  
PMID:29568061   PMID:29576527   PMID:30021884   PMID:30194290   PMID:32513696   PMID:32694731   PMID:33961781   PMID:34079125   PMID:34369648   PMID:34597346   PMID:35914814   PMID:37689310  


Genomics

Comparative Map Data
VPS54
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38263,892,150 - 64,019,428 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl263,892,146 - 64,019,428 (-)EnsemblGRCh38hg38GRCh38
GRCh37264,119,284 - 64,246,562 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36263,973,171 - 64,099,718 (-)NCBINCBI36Build 36hg18NCBI36
Build 34264,031,317 - 64,157,865NCBI
Celera263,964,934 - 64,091,495 (-)NCBICelera
Cytogenetic Map2p15-p14NCBI
HuRef263,859,380 - 63,986,062 (-)NCBIHuRef
CHM1_1264,049,942 - 64,176,502 (-)NCBICHM1_1
T2T-CHM13v2.0263,899,706 - 64,027,065 (-)NCBIT2T-CHM13v2.0
Vps54
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391121,189,032 - 21,271,133 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1121,189,281 - 21,271,136 (+)EnsemblGRCm39 Ensembl
GRCm381121,239,032 - 21,321,133 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1121,239,281 - 21,321,136 (+)EnsemblGRCm38mm10GRCm38
MGSCv371121,138,892 - 21,221,136 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361121,139,284 - 21,221,136 (+)NCBIMGSCv36mm8
Celera1123,411,563 - 23,469,500 (+)NCBICelera
Cytogenetic Map11A3.1NCBI
cM Map1113.89NCBI
Vps54
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81499,580,120 - 99,657,178 (+)NCBIGRCr8
mRatBN7.21495,378,821 - 95,455,871 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1495,378,012 - 95,455,857 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1499,748,500 - 99,803,139 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.014100,988,838 - 101,043,480 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01497,462,359 - 97,517,004 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.014106,153,407 - 106,207,715 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14106,153,575 - 106,207,658 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.014106,220,200 - 106,274,489 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414102,018,126 - 102,072,258 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.114102,037,336 - 102,091,469 (+)NCBI
Celera1494,414,915 - 94,468,850 (+)NCBICelera
Cytogenetic Map14q22NCBI
Vps54
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542420,327,754 - 20,445,980 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542420,329,009 - 20,443,652 (+)NCBIChiLan1.0ChiLan1.0
VPS54
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21262,380,379 - 62,507,197 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A62,384,330 - 62,510,395 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A63,959,930 - 64,087,102 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A65,085,093 - 65,176,657 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A65,086,374 - 65,176,634 (-)Ensemblpanpan1.1panPan2
VPS54
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11063,598,373 - 63,676,753 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1063,599,229 - 63,676,747 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1063,487,248 - 63,565,630 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01064,607,383 - 64,685,416 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1064,608,155 - 64,683,345 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11064,289,180 - 64,367,317 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01064,598,125 - 64,676,956 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01064,890,757 - 64,968,754 (-)NCBIUU_Cfam_GSD_1.0
Vps54
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629219,648,881 - 19,735,890 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364918,833,285 - 8,922,711 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364918,835,397 - 8,922,403 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
VPS54
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl377,856,138 - 77,975,429 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1377,856,093 - 77,978,194 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2381,716,210 - 81,780,374 (+)NCBISscrofa10.2Sscrofa10.2susScr3
VPS54
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11443,000,960 - 43,127,129 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1443,008,915 - 43,125,850 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604568,734,694 - 68,867,307 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Vps54
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247629,457,705 - 9,563,779 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247629,457,283 - 9,570,311 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in VPS54
45 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2p15-14(chr2:63867188-64294742)x3 copy number gain See cases [RCV000052661] Chr2:63867188..64294742 [GRCh38]
Chr2:64094322..64521876 [GRCh37]
Chr2:63947826..64375380 [NCBI36]
Chr2:2p15-14		 uncertain significance
GRCh38/hg38 2p16.1-14(chr2:58873039-64190332)x1 copy number loss See cases [RCV000054022] Chr2:58873039..64190332 [GRCh38]
Chr2:59100174..64417466 [GRCh37]
Chr2:58953678..64270970 [NCBI36]
Chr2:2p16.1-14		 pathogenic
GRCh38/hg38 2p15-14(chr2:63311999-67309291)x1 copy number loss See cases [RCV000054054] Chr2:63311999..67309291 [GRCh38]
Chr2:63539134..67536423 [GRCh37]
Chr2:63392638..67389927 [NCBI36]
Chr2:2p15-14		 pathogenic
NM_001005739.1(VPS54):c.-21+1737G>T single nucleotide variant Lung cancer [RCV000092263] Chr2:64017201 [GRCh38]
Chr2:64244335 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.2228+14T>A single nucleotide variant not provided [RCV001580032]|not specified [RCV001727913] Chr2:63916886 [GRCh38]
Chr2:64144020 [GRCh37]
Chr2:2p14		 benign|likely benign
GRCh38/hg38 2p16.1-11.2(chr2:58279519-83586962)x3 copy number gain See cases [RCV000136053] Chr2:58279519..83586962 [GRCh38]
Chr2:58506654..83814086 [GRCh37]
Chr2:58360158..83667597 [NCBI36]
Chr2:2p16.1-11.2		 pathogenic
GRCh38/hg38 2p16.3-11.2(chr2:47620388-86702722)x3 copy number gain See cases [RCV000137586] Chr2:47620388..86702722 [GRCh38]
Chr2:47847527..86929845 [GRCh37]
Chr2:47701031..86783356 [NCBI36]
Chr2:2p16.3-11.2		 uncertain significance
GRCh38/hg38 2p25.1-11.2(chr2:7495123-87705899)x3 copy number gain See cases [RCV000141494] Chr2:7495123..87705899 [GRCh38]
Chr2:7635254..88005418 [GRCh37]
Chr2:7552705..87786533 [NCBI36]
Chr2:2p25.1-11.2		 benign
GRCh37/hg19 2p25.3-q37.3(chr2:14238-243048760)x3 copy number gain not provided [RCV000752802] Chr2:14238..243048760 [GRCh37]
Chr2:2p25.3-q37.3		 pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:15672-243101834)x3 copy number gain not provided [RCV000752804] Chr2:15672..243101834 [GRCh37]
Chr2:2p25.3-q37.3		 pathogenic
GRCh37/hg19 2p15-11.2(chr2:62245236-86978895)x3 copy number gain See cases [RCV000448688] Chr2:62245236..86978895 [GRCh37]
Chr2:2p15-11.2		 pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384) copy number gain See cases [RCV000512056] Chr2:12771..242783384 [GRCh37]
Chr2:2p25.3-q37.3		 pathogenic
GRCh37/hg19 2p15-14(chr2:63234780-67908846)x1 copy number loss See cases [RCV000511763] Chr2:63234780..67908846 [GRCh37]
Chr2:2p15-14		 pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384)x3 copy number gain See cases [RCV000511212] Chr2:12771..242783384 [GRCh37]
Chr2:2p25.3-q37.3		 pathogenic
GRCh37/hg19 2p15-14(chr2:61701437-65731084)x1 copy number loss See cases [RCV000511169] Chr2:61701437..65731084 [GRCh37]
Chr2:2p15-14		 likely pathogenic
NM_016516.3(VPS54):c.134C>T (p.Thr45Ile) single nucleotide variant not specified [RCV004312062] Chr2:63983866 [GRCh38]
Chr2:64211000 [GRCh37]
Chr2:2p14		 uncertain significance
Single allele duplication not provided [RCV000677942] Chr2:63671346..85698002 [GRCh37]
Chr2:2p15-11.2		 pathogenic
Single allele deletion not provided [RCV000714264] Chr2:40608411..146900718 [GRCh37]
Chr2:2p22.1-q22.3		 likely pathogenic
GRCh37/hg19 2p15-14(chr2:64016747-64503895)x3 copy number gain not provided [RCV000740473] Chr2:64016747..64503895 [GRCh37]
Chr2:2p15-14		 benign
GRCh37/hg19 2p15-14(chr2:64098730-64800452)x3 copy number gain not provided [RCV000740475] Chr2:64098730..64800452 [GRCh37]
Chr2:2p15-14		 benign
NM_016516.3(VPS54):c.2626-7C>T single nucleotide variant not provided [RCV000938163] Chr2:63899588 [GRCh38]
Chr2:64126722 [GRCh37]
Chr2:2p15		 benign
NM_016516.3(VPS54):c.1721C>G (p.Pro574Arg) single nucleotide variant not provided [RCV000997150] Chr2:63933691 [GRCh38]
Chr2:64160825 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.234C>T (p.Asn78=) single nucleotide variant not provided [RCV000946616] Chr2:63981790 [GRCh38]
Chr2:64208924 [GRCh37]
Chr2:2p14		 benign
NM_016516.3(VPS54):c.1946C>G (p.Thr649Ser) single nucleotide variant not provided [RCV000997148] Chr2:63920551 [GRCh38]
Chr2:64147685 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.1057A>G (p.Met353Val) single nucleotide variant not provided [RCV000997151] Chr2:63949117 [GRCh38]
Chr2:64176251 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.501G>C (p.Met167Ile) single nucleotide variant Tooth agenesis [RCV000993577] Chr2:63965958 [GRCh38]
Chr2:64193092 [GRCh37]
Chr2:2p14		 uncertain significance
GRCh37/hg19 2p15-14(chr2:63536353-65793944)x1 copy number loss not provided [RCV000848078] Chr2:63536353..65793944 [GRCh37]
Chr2:2p15-14		 pathogenic
NM_016516.3(VPS54):c.1770A>G (p.Ser590=) single nucleotide variant not provided [RCV000997149] Chr2:63921305 [GRCh38]
Chr2:64148439 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.894G>C (p.Gln298His) single nucleotide variant not specified [RCV004300613] Chr2:63962174 [GRCh38]
Chr2:64189308 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.1682C>G (p.Ser561Cys) single nucleotide variant not provided [RCV000955929] Chr2:63933730 [GRCh38]
Chr2:64160864 [GRCh37]
Chr2:2p14		 benign
NM_016516.3(VPS54):c.2625+9T>A single nucleotide variant not provided [RCV001579416] Chr2:63912336 [GRCh38]
Chr2:64139470 [GRCh37]
Chr2:2p14		 likely benign
NM_016516.3(VPS54):c.2228+13T>G single nucleotide variant not provided [RCV001579557]|not specified [RCV001726603] Chr2:63916887 [GRCh38]
Chr2:64144021 [GRCh37]
Chr2:2p14		 benign|likely benign
NM_016516.3(VPS54):c.636T>C (p.Tyr212=) single nucleotide variant not specified [RCV001580025] Chr2:63962432 [GRCh38]
Chr2:64189566 [GRCh37]
Chr2:2p14		 benign
NM_016516.3(VPS54):c.2736G>T (p.Met912Ile) single nucleotide variant not specified [RCV001579956] Chr2:63897588 [GRCh38]
Chr2:64124722 [GRCh37]
Chr2:2p15		 benign
NC_000002.11:g.(?_62991401)_(64335444_?)dup duplication Bardet-Biedl syndrome [RCV001372441] Chr2:62991401..64335444 [GRCh37]
Chr2:2p15-14		 uncertain significance
GRCh37/hg19 2p25.3-q37.3(chr2:1-243199373) copy number gain Mosaic trisomy 2 [RCV002280628] Chr2:1..243199373 [GRCh37]
Chr2:2p25.3-q37.3		 pathogenic
GRCh37/hg19 2p14(chr2:64103740-64802404) copy number gain not specified [RCV002052815] Chr2:64103740..64802404 [GRCh37]
Chr2:2p14		 uncertain significance
GRCh37/hg19 2p25.1-q13(chr2:11504318-111365996)x1 copy number loss See cases [RCV002287563] Chr2:11504318..111365996 [GRCh37]
Chr2:2p25.1-q13		 pathogenic
NM_016516.3(VPS54):c.922T>A (p.Ser308Thr) single nucleotide variant not specified [RCV004305363] Chr2:63962146 [GRCh38]
Chr2:64189280 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.301A>G (p.Thr101Ala) single nucleotide variant not specified [RCV004294172] Chr2:63981723 [GRCh38]
Chr2:64208857 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.1414A>C (p.Ile472Leu) single nucleotide variant not specified [RCV004118308] Chr2:63933998 [GRCh38]
Chr2:64161132 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.452C>T (p.Thr151Ile) single nucleotide variant not specified [RCV004095728] Chr2:63972171 [GRCh38]
Chr2:64199305 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.1592C>T (p.Ala531Val) single nucleotide variant not specified [RCV004116338] Chr2:63933820 [GRCh38]
Chr2:64160954 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.2507A>G (p.Gln836Arg) single nucleotide variant not specified [RCV004209266] Chr2:63912577 [GRCh38]
Chr2:64139711 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.76C>G (p.Pro26Ala) single nucleotide variant not specified [RCV004158096] Chr2:63983924 [GRCh38]
Chr2:64211058 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.77C>T (p.Pro26Leu) single nucleotide variant not specified [RCV004078353] Chr2:63983923 [GRCh38]
Chr2:64211057 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.2286C>G (p.Ile762Met) single nucleotide variant not specified [RCV004094887] Chr2:63914230 [GRCh38]
Chr2:64141364 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.1838G>A (p.Arg613Gln) single nucleotide variant not specified [RCV004148329] Chr2:63921237 [GRCh38]
Chr2:64148371 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.2194C>G (p.Leu732Val) single nucleotide variant not specified [RCV004148330] Chr2:63916934 [GRCh38]
Chr2:64144068 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.589C>T (p.Arg197Cys) single nucleotide variant not specified [RCV004101286] Chr2:63965870 [GRCh38]
Chr2:64193004 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.56T>C (p.Phe19Ser) single nucleotide variant not specified [RCV004218291] Chr2:63983944 [GRCh38]
Chr2:64211078 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.790A>G (p.Lys264Glu) single nucleotide variant not specified [RCV004152627] Chr2:63962278 [GRCh38]
Chr2:64189412 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.1595T>C (p.Val532Ala) single nucleotide variant not specified [RCV004241477] Chr2:63933817 [GRCh38]
Chr2:64160951 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.891C>G (p.His297Gln) single nucleotide variant not specified [RCV004151974] Chr2:63962177 [GRCh38]
Chr2:64189311 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.2030A>G (p.Glu677Gly) single nucleotide variant not specified [RCV004219089] Chr2:63920467 [GRCh38]
Chr2:64147601 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.718G>A (p.Glu240Lys) single nucleotide variant not specified [RCV004217636] Chr2:63962350 [GRCh38]
Chr2:64189484 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.1847A>G (p.Lys616Arg) single nucleotide variant not specified [RCV004173349] Chr2:63921228 [GRCh38]
Chr2:64148362 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.1554A>G (p.Ile518Met) single nucleotide variant not specified [RCV004276875] Chr2:63933858 [GRCh38]
Chr2:64160992 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.1956C>G (p.Ile652Met) single nucleotide variant not specified [RCV004256047] Chr2:63920541 [GRCh38]
Chr2:64147675 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.1567G>A (p.Gly523Ser) single nucleotide variant not specified [RCV004250766] Chr2:63933845 [GRCh38]
Chr2:64160979 [GRCh37]
Chr2:2p14		 likely benign
NM_016516.3(VPS54):c.1328A>T (p.Asn443Ile) single nucleotide variant not specified [RCV004283129] Chr2:63942535 [GRCh38]
Chr2:64169669 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.1703C>T (p.Thr568Ile) single nucleotide variant not specified [RCV004258475] Chr2:63933709 [GRCh38]
Chr2:64160843 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.2386G>C (p.Val796Leu) single nucleotide variant not specified [RCV004349669] Chr2:63913259 [GRCh38]
Chr2:64140393 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.1513G>A (p.Asp505Asn) single nucleotide variant not specified [RCV004484906] Chr2:63933899 [GRCh38]
Chr2:64161033 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.562T>G (p.Phe188Val) single nucleotide variant not specified [RCV004484913] Chr2:63965897 [GRCh38]
Chr2:64193031 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.1864G>A (p.Ala622Thr) single nucleotide variant not specified [RCV004484908] Chr2:63921211 [GRCh38]
Chr2:64148345 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.2474G>A (p.Arg825Gln) single nucleotide variant not specified [RCV004484910] Chr2:63912610 [GRCh38]
Chr2:64139744 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.707C>G (p.Thr236Ser) single nucleotide variant not specified [RCV004484914] Chr2:63962361 [GRCh38]
Chr2:64189495 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.1574G>C (p.Gly525Ala) single nucleotide variant not specified [RCV004484907] Chr2:63933838 [GRCh38]
Chr2:64160972 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.1933T>C (p.Phe645Leu) single nucleotide variant not specified [RCV004484909] Chr2:63920564 [GRCh38]
Chr2:64147698 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.2858C>T (p.Thr953Ile) single nucleotide variant not specified [RCV004484911] Chr2:63893506 [GRCh38]
Chr2:64120640 [GRCh37]
Chr2:2p15		 uncertain significance
NM_016516.3(VPS54):c.826C>G (p.Leu276Val) single nucleotide variant not specified [RCV004484915] Chr2:63962242 [GRCh38]
Chr2:64189376 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.1004G>A (p.Ser335Asn) single nucleotide variant not specified [RCV004484905] Chr2:63962064 [GRCh38]
Chr2:64189198 [GRCh37]
Chr2:2p14		 uncertain significance
NM_016516.3(VPS54):c.478G>C (p.Glu160Gln) single nucleotide variant not specified [RCV004484912] Chr2:63968971 [GRCh38]
Chr2:64196105 [GRCh37]
Chr2:2p14		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:755
Count of miRNA genes:382
Interacting mature miRNAs:404
Transcripts:ENST00000272322, ENST00000354504, ENST00000409558, ENST00000416400
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
D2S147  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37264,165,069 - 64,165,179UniSTSGRCh37
Build 36264,018,573 - 64,018,683RGDNCBI36
Celera264,010,337 - 64,010,447RGD
HuRef263,904,795 - 63,904,905UniSTS
Marshfield Genetic Map282.29UniSTS
Marshfield Genetic Map282.29RGD
Genethon Genetic Map285.7UniSTS
TNG Radiation Hybrid Map240272.0UniSTS
Stanford-G3 RH Map22566.0UniSTS
GeneMap99-GB4 RH Map2198.15UniSTS
Whitehead-YAC Contig Map2 UniSTS
NCBI RH Map2349.4UniSTS
GeneMap99-G3 RH Map22523.0UniSTS
RH93801  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37264,120,398 - 64,120,535UniSTSGRCh37
Build 36263,973,902 - 63,974,039RGDNCBI36
Celera263,965,666 - 63,965,803RGD
Cytogenetic Map2p13-p14UniSTS
HuRef263,860,112 - 63,860,249UniSTS
GeneMap99-GB4 RH Map2194.14UniSTS
RH46124  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37264,119,437 - 64,119,568UniSTSGRCh37
Build 36263,972,941 - 63,973,072RGDNCBI36
Celera263,964,704 - 63,964,835RGD
Cytogenetic Map2p13-p14UniSTS
HuRef263,859,150 - 63,859,281UniSTS
GeneMap99-GB4 RH Map2202.66UniSTS
NCBI RH Map2349.4UniSTS
D2S147  
Human AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map2p13-p14UniSTS
TNG Radiation Hybrid Map240272.0UniSTS
Stanford-G3 RH Map22566.0UniSTS
GeneMap99-GB4 RH Map2198.15UniSTS
NCBI RH Map2349.4UniSTS
GeneMap99-G3 RH Map22523.0UniSTS


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 adipose tissue appendage entire extraembryonic component
High
Medium 2254 1484 1447 373 1205 218 3594 1037 1667 329 1429 1598 168 1188 2048 4
Low 178 1493 276 249 736 246 761 1156 2041 89 19 10 3 16 740
Below cutoff 7 7

Sequence

Nucleotide Sequences
RefSeq Transcripts NG_042277 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001005739 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_016516 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017004316 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047444727 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047444728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047444729 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047444730 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047444731 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047444732 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054342519 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054342520 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054342521 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054342522 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054342523 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054342524 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001738770 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_002959306 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_007076389 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_008486393 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_244939 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC092588 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF102177 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK002205 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK025545 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK094019 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK124436 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK292669 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK292889 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL137604 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL359939 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL514510 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AW452246 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY444798 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC030275 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC041868 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068276 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CR749701 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000272322   ⟹   ENSP00000272322
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl263,892,150 - 64,019,428 (-)Ensembl
RefSeq Acc Id: ENST00000354504   ⟹   ENSP00000346499
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl263,892,901 - 63,975,602 (-)Ensembl
RefSeq Acc Id: ENST00000409558   ⟹   ENSP00000386980
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl263,892,146 - 64,019,072 (-)Ensembl
RefSeq Acc Id: ENST00000416400   ⟹   ENSP00000414725
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl263,893,072 - 63,919,930 (-)Ensembl
RefSeq Acc Id: NM_001005739   ⟹   NP_001005739
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38263,892,150 - 64,019,428 (-)NCBI
GRCh37264,119,280 - 64,246,526 (-)NCBI
Build 36263,973,171 - 64,099,718 (-)NCBI Archive
Celera263,964,934 - 64,091,495 (-)RGD
HuRef263,859,380 - 63,986,062 (-)RGD
CHM1_1264,049,942 - 64,176,502 (-)NCBI
T2T-CHM13v2.0263,899,706 - 64,027,065 (-)NCBI
Sequence:
RefSeq Acc Id: NM_016516   ⟹   NP_057600
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38263,892,150 - 64,019,428 (-)NCBI
GRCh37264,119,280 - 64,246,526 (-)NCBI
Build 36263,973,171 - 64,099,718 (-)NCBI Archive
Celera263,964,934 - 64,091,495 (-)RGD
HuRef263,859,380 - 63,986,062 (-)RGD
CHM1_1264,049,942 - 64,176,502 (-)NCBI
T2T-CHM13v2.0263,899,706 - 64,027,065 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017004316   ⟹   XP_016859805
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38263,892,150 - 64,019,428 (-)NCBI
Sequence:
RefSeq Acc Id: XM_047444727   ⟹   XP_047300683
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38263,892,150 - 64,012,454 (-)NCBI
RefSeq Acc Id: XM_047444728   ⟹   XP_047300684
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38263,892,150 - 64,019,428 (-)NCBI
RefSeq Acc Id: XM_047444729   ⟹   XP_047300685
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38263,892,150 - 64,012,454 (-)NCBI
RefSeq Acc Id: XM_047444730   ⟹   XP_047300686
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38263,892,150 - 64,012,454 (-)NCBI
RefSeq Acc Id: XM_047444731   ⟹   XP_047300687
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38263,921,263 - 64,019,428 (-)NCBI
RefSeq Acc Id: XM_047444732   ⟹   XP_047300688
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38263,938,892 - 64,019,428 (-)NCBI
RefSeq Acc Id: XM_054342519   ⟹   XP_054198494
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0263,899,706 - 64,027,065 (-)NCBI
RefSeq Acc Id: XM_054342520   ⟹   XP_054198495
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0263,899,706 - 64,021,119 (-)NCBI
RefSeq Acc Id: XM_054342521   ⟹   XP_054198496
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0263,899,706 - 64,027,065 (-)NCBI
RefSeq Acc Id: XM_054342522   ⟹   XP_054198497
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0263,899,706 - 64,021,119 (-)NCBI
RefSeq Acc Id: XM_054342523   ⟹   XP_054198498
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0263,928,846 - 64,027,065 (-)NCBI
RefSeq Acc Id: XM_054342524   ⟹   XP_054198499
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0263,946,336 - 64,027,065 (-)NCBI
RefSeq Acc Id: XR_007076389
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38263,913,224 - 64,019,428 (-)NCBI
RefSeq Acc Id: XR_008486393
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0263,920,805 - 64,027,065 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001005739 (Get FASTA)   NCBI Sequence Viewer  
  NP_057600 (Get FASTA)   NCBI Sequence Viewer  
  XP_016859805 (Get FASTA)   NCBI Sequence Viewer  
  XP_047300683 (Get FASTA)   NCBI Sequence Viewer  
  XP_047300684 (Get FASTA)   NCBI Sequence Viewer  
  XP_047300685 (Get FASTA)   NCBI Sequence Viewer  
  XP_047300686 (Get FASTA)   NCBI Sequence Viewer  
  XP_047300687 (Get FASTA)   NCBI Sequence Viewer  
  XP_047300688 (Get FASTA)   NCBI Sequence Viewer  
  XP_054198494 (Get FASTA)   NCBI Sequence Viewer  
  XP_054198495 (Get FASTA)   NCBI Sequence Viewer  
  XP_054198496 (Get FASTA)   NCBI Sequence Viewer  
  XP_054198497 (Get FASTA)   NCBI Sequence Viewer  
  XP_054198498 (Get FASTA)   NCBI Sequence Viewer  
  XP_054198499 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF37319 (Get FASTA)   NCBI Sequence Viewer  
  AAH30275 (Get FASTA)   NCBI Sequence Viewer  
  AAH41868 (Get FASTA)   NCBI Sequence Viewer  
  AAS20945 (Get FASTA)   NCBI Sequence Viewer  
  BAA92134 (Get FASTA)   NCBI Sequence Viewer  
  BAF85358 (Get FASTA)   NCBI Sequence Viewer  
  BAF85578 (Get FASTA)   NCBI Sequence Viewer  
  CAB70837 (Get FASTA)   NCBI Sequence Viewer  
  CAB95772 (Get FASTA)   NCBI Sequence Viewer  
  CAH18479 (Get FASTA)   NCBI Sequence Viewer  
  EAW99952 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000272322
  ENSP00000272322.4
  ENSP00000346499
  ENSP00000346499.3
  ENSP00000386980
  ENSP00000386980.3
  ENSP00000414725.2
GenBank Protein Q9P1Q0 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_057600   ⟸   NM_016516
- Peptide Label: isoform 1
- UniProtKB: Q9NT07 (UniProtKB/Swiss-Prot),   Q9NPV0 (UniProtKB/Swiss-Prot),   Q8N6G3 (UniProtKB/Swiss-Prot),   Q86YF7 (UniProtKB/Swiss-Prot),   Q5VIR5 (UniProtKB/Swiss-Prot),   Q9NUJ0 (UniProtKB/Swiss-Prot),   Q9P1Q0 (UniProtKB/Swiss-Prot),   A8K9F4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001005739   ⟸   NM_001005739
- Peptide Label: isoform 2
- UniProtKB: A8KA24 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_016859805   ⟸   XM_017004316
- Peptide Label: isoform X3
- UniProtKB: A8KA24 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000414725   ⟸   ENST00000416400
RefSeq Acc Id: ENSP00000272322   ⟸   ENST00000272322
RefSeq Acc Id: ENSP00000346499   ⟸   ENST00000354504
RefSeq Acc Id: ENSP00000386980   ⟸   ENST00000409558
RefSeq Acc Id: XP_047300684   ⟸   XM_047444728
- Peptide Label: isoform X1
- UniProtKB: Q9P1Q0 (UniProtKB/Swiss-Prot),   Q9NT07 (UniProtKB/Swiss-Prot),   Q9NPV0 (UniProtKB/Swiss-Prot),   Q8N6G3 (UniProtKB/Swiss-Prot),   Q86YF7 (UniProtKB/Swiss-Prot),   Q5VIR5 (UniProtKB/Swiss-Prot),   Q9NUJ0 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_047300686   ⟸   XM_047444730
- Peptide Label: isoform X3
RefSeq Acc Id: XP_047300683   ⟸   XM_047444727
- Peptide Label: isoform X1
- UniProtKB: Q9P1Q0 (UniProtKB/Swiss-Prot),   Q9NT07 (UniProtKB/Swiss-Prot),   Q9NPV0 (UniProtKB/Swiss-Prot),   Q8N6G3 (UniProtKB/Swiss-Prot),   Q86YF7 (UniProtKB/Swiss-Prot),   Q5VIR5 (UniProtKB/Swiss-Prot),   Q9NUJ0 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_047300685   ⟸   XM_047444729
- Peptide Label: isoform X2
RefSeq Acc Id: XP_047300687   ⟸   XM_047444731
- Peptide Label: isoform X4
RefSeq Acc Id: XP_047300688   ⟸   XM_047444732
- Peptide Label: isoform X5
RefSeq Acc Id: XP_054198496   ⟸   XM_054342521
- Peptide Label: isoform X3
RefSeq Acc Id: XP_054198494   ⟸   XM_054342519
- Peptide Label: isoform X1
- UniProtKB: Q9P1Q0 (UniProtKB/Swiss-Prot),   Q9NT07 (UniProtKB/Swiss-Prot),   Q9NPV0 (UniProtKB/Swiss-Prot),   Q8N6G3 (UniProtKB/Swiss-Prot),   Q86YF7 (UniProtKB/Swiss-Prot),   Q5VIR5 (UniProtKB/Swiss-Prot),   Q9NUJ0 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_054198497   ⟸   XM_054342522
- Peptide Label: isoform X3
RefSeq Acc Id: XP_054198495   ⟸   XM_054342520
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054198498   ⟸   XM_054342523
- Peptide Label: isoform X4
RefSeq Acc Id: XP_054198499   ⟸   XM_054342524
- Peptide Label: isoform X5
Protein Domains
Vacuolar protein sorting-associated protein 54 C-   Vacuolar protein sorting-associated protein 54 N-

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9P1Q0-F1-model_v2 AlphaFold Q9P1Q0 1-977 view protein structure

Promoters
RGD ID:6860454
Promoter ID:EPDNEW_H3392
Type:initiation region
Name:VPS54_1
Description:VPS54, GARP complex subunit
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H3393  EPDNEW_H3394  EPDNEW_H3395  EPDNEW_H3396  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38263,919,881 - 63,919,941EPDNEW
RGD ID:6860456
Promoter ID:EPDNEW_H3393
Type:multiple initiation site
Name:VPS54_5
Description:VPS54, GARP complex subunit
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H3392  EPDNEW_H3394  EPDNEW_H3395  EPDNEW_H3396  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38263,975,600 - 63,975,660EPDNEW
RGD ID:6860458
Promoter ID:EPDNEW_H3394
Type:multiple initiation site
Name:VPS54_3
Description:VPS54, GARP complex subunit
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H3392  EPDNEW_H3393  EPDNEW_H3395  EPDNEW_H3396  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38264,004,021 - 64,004,081EPDNEW
RGD ID:6860460
Promoter ID:EPDNEW_H3395
Type:initiation region
Name:VPS54_2
Description:VPS54, GARP complex subunit
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H3392  EPDNEW_H3393  EPDNEW_H3394  EPDNEW_H3396  
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38264,019,027 - 64,019,087EPDNEW
RGD ID:6798436
Promoter ID:HG_KWN:32916
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:ENST00000394400,   NM_001005739,   NM_016516
Position:
Human AssemblyChrPosition (strand)Source
Build 36264,099,839 - 64,100,339 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:18652 AgrOrtholog
COSMIC VPS54 COSMIC
Ensembl Genes ENSG00000143952 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000272322 ENTREZGENE
  ENST00000272322.9 UniProtKB/Swiss-Prot
  ENST00000354504 ENTREZGENE
  ENST00000354504.7 UniProtKB/Swiss-Prot
  ENST00000409558 ENTREZGENE
  ENST00000409558.8 UniProtKB/Swiss-Prot
  ENST00000416400.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1280.130 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  6.10.250.860 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000143952 GTEx
HGNC ID HGNC:18652 ENTREZGENE
Human Proteome Map VPS54 Human Proteome Map
InterPro Vps54 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vps54_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VPS54_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:51542 UniProtKB/Swiss-Prot
NCBI Gene 51542 ENTREZGENE
OMIM 614633 OMIM
PANTHER PTHR12965 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 54 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Vps54 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Vps54_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA134920394 PharmGKB
UniProt A0A0A0MT48_HUMAN UniProtKB/TrEMBL
  A8K9F4 ENTREZGENE, UniProtKB/TrEMBL
  A8KA24 ENTREZGENE, UniProtKB/TrEMBL
  Q5VIR5 ENTREZGENE
  Q86YF7 ENTREZGENE
  Q8N6G3 ENTREZGENE
  Q9NPV0 ENTREZGENE
  Q9NT07 ENTREZGENE
  Q9NUJ0 ENTREZGENE
  Q9P1Q0 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q5VIR5 UniProtKB/Swiss-Prot
  Q86YF7 UniProtKB/Swiss-Prot
  Q8N6G3 UniProtKB/Swiss-Prot
  Q9NPV0 UniProtKB/Swiss-Prot
  Q9NT07 UniProtKB/Swiss-Prot
  Q9NUJ0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-01-29 VPS54  VPS54 subunit of GARP complex  VPS54  VPS54, GARP complex subunit  Symbol and/or name change 5135510 APPROVED
2016-03-07 VPS54  VPS54, GARP complex subunit  VPS54  VPS54 GARP complex subunit  Symbol and/or name change 5135510 APPROVED
2015-11-24 VPS54  VPS54 GARP complex subunit  VPS54  vacuolar protein sorting 54 homolog (S. cerevisiae)  Symbol and/or name change 5135510 APPROVED