VPS51 (VPS51 subunit of GARP complex)

Gene Gene information from NCBI Gene database.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID 738
Gene name VPS51 subunit of GARP complex
Gene symbol VPS51
Synonyms (NCBI Gene)
ANG2ANG3C11orf2C11orf3FFRPCH13
Chromosome 11
Chromosome location 11q13.1
Summary This gene encodes a member of the vacuolar protein sorting-associated protein 51 family. The encoded protein is a component of the Golgi-associated retrograde protein complex which acts as a tethering factor for carriers in retrograde transport from the e
SNPs SNP information provided by dbSNP.
2
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all (2)
SNP ID Visualize variation Clinical significance Consequence
rs752863502 TCT>- Pathogenic Inframe deletion, coding sequence variant, non coding transcript variant
rs1203009966 C>T Pathogenic Coding sequence variant, non coding transcript variant, missense variant
miRNA miRNA information provided by mirtarbase database.
234
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all (234)
miRTarBase ID miRNA Experiments Reference
MIRT032314 hsa-let-7b-5p Proteomics 18668040
MIRT047211 hsa-miR-182-5p CLASH 23622248
MIRT043055 hsa-miR-324-5p CLASH 23622248
MIRT438384 hsa-miR-125a-5p Luciferase reporter assay 25172656
MIRT438383 hsa-miR-125b-5p Luciferase reporter assay 25172656
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
37
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all (37)
GO ID Ontology Definition Evidence Reference
GO:0000938 Component GARP complex IBA
GO:0000938 Component GARP complex IDA 20685960, 25799061
GO:0000938 Component GARP complex NAS 25799061
GO:0005515 Function Protein binding IPI 3172165, 20685960, 23932592, 25799061
GO:0005730 Component Nucleolus IDA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
MIM HGNC e!Ensembl
615738 1172 ENSG00000149823
Protein Protein information from UniProt database.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9UID3
Protein name Vacuolar protein sorting-associated protein 51 homolog (Another new gene 2 protein) (Protein fat-free homolog)
Protein function Acts as a component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). The GARP complex is required for the maintenance of protein retrieval from endosomes to the TGN, aci
PDB 4J2C
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF08700 Vps51 63 → 148 Family
Sequence 
MAAAAAAGPSPGSGPGDSPEGPEGEAPERRRKAHGMLKLYYGLSEGEAAGRPAGPDPLDP
TDLNGAHFDPEVYLDKLRRECPLAQLMDSETDMVRQIRALDSDMQTLVYENYNKFISATD
TIRKMKNDFRKMEDEMDRLATNMAVITDFSARISATLQDRHERITKLAGVHALLRKLQFL
FELPSRLTKCVELGAYGQAVRYQGRAQAVLQQYQHLPSFRAIQDDCQVITARLAQQLRQR
FREGGSGAPEQAECVELLLALGEPAEELCEEFLAHARGRLEKELRNLEAELGPSPPAPDV
LEFTDHGGSGFVGGLCQVAAAYQELFAAQGPAGAEKLAAFARQLGSRYFALVERRLAQEQ
GGGDNSLLVRALDRFHRRLRAPGALLAAAGLADAATEIVERVARERLGHHLQGLRAAFLG
CLTDVRQALAAPRVAGKEGPGLAELLANVASSILSHIKASLAAVHLFTAKEVSFSNKPYF
RGEFCSQGVREGLIVGFVHSMCQTAQSFCDSPGEKGGATPPALLLLLSRLCLDYETATIS
YILTLTDEQFLVQDQFPVTPVSTLCAEARETARRLLTHYVKVQGLVISQMLRKSVETRDW
LSTLEPRNVRAVMKRVVEDTTAIDVQVGLLYEEGVRKAQSSDSSKRTFSVYSSSRQQGRY
APSYTPSAPMDTNLLSNIQKLFSERIDVFSPVEFNKVSVLTGIIKISLKTLLECVRLRTF
GRFGLQQVQVDCHFLQLYLWRFVADEELVHLLLDEVVASAALRCPDPVPMEPSVVEVICE
RG
Sequence length 782
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
  Reactome
    Retrograde transport at the Trans-Golgi-Network
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
3
Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Show/Hide Causal Diseases (1)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Pontocerebellar hypoplasia, type 13 Pathogenic rs1590815040, rs1203009966, rs752863502 RCV000852344
RCV000852345
RCV000852346
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Show/Hide Unknown Diseases (2)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
GOUT — GWAS catalog
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
VPS51-related disorder Benign; Likely benign ClinVar
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Show/Hide Text Mining Associations (199)
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acute Coronary Syndrome Coronary Syndrome BEFREE 31390228, 31400061
★★★★★
★☆☆☆☆
Found in Text Mining only
Addison Disease Addison`s Disease BEFREE 31075757
★★★★★
★☆☆☆☆
Found in Text Mining only
Adenocarcinoma of pancreas Pancreatic adenocarcinoma BEFREE 15501112
★★★★★
★☆☆☆☆
Found in Text Mining only
Anaplasia Anaplasia BEFREE 31348822
★★★★★
★☆☆☆☆
Found in Text Mining only
Anemia Anemia BEFREE 30629717
★★★★★
★☆☆☆☆
Found in Text Mining only
Anemia, Sickle Cell Anemia BEFREE 25574809, 30994508
★★★★★
★☆☆☆☆
Found in Text Mining only
ANOPHTHALMIA AND PULMONARY HYPOPLASIA Syndromic microphthalmia BEFREE 21685330
★★★★★
★☆☆☆☆
Found in Text Mining only
Anxiety Anxiety Disorder BEFREE 31001119
★★★★★
★☆☆☆☆
Found in Text Mining only
Anxiety Disorders Anxiety Disorder BEFREE 31001119
★★★★★
★☆☆☆☆
Found in Text Mining only
Aortic Aneurysm Aortic Aneurysm BEFREE 30943775
★★★★★
★☆☆☆☆
Found in Text Mining only