VAMP7

vesicle associated membrane protein 7, the group of Pseudoautosomal region 2|Vesicle associated membrane proteins

Basic information

Region (hg38): Y:57067865-57130289

Previous symbols: [ "SYBL1" ]

Links

ENSG00000292366 ∙ NCBI:6845 ∙ OMIM:300053 ∙ HGNC:11486 ∙ Uniprot:P51809 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VAMP7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VAMP7 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense				6	2	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	0	6	6

Variants in VAMP7

This is a list of pathogenic ClinVar variants found in the VAMP7 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
Y-57084754-C-G			Benign (Dec 31, 2019)
Y-57087038-G-A			Likely benign (Dec 03, 2018)
Y-57087054-T-C			Benign (Dec 31, 2019)
Y-57126292-T-C		VAMP7-related disorder	Likely benign (Dec 31, 2019)
Y-57126304-C-T			Likely benign (Jun 01, 2023)
Y-57128393-G-C		VAMP7-related disorder	Benign (Mar 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VAMP7	protein_coding	protein_coding	ENST00000262640	6	62478

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0138	0.959	125577	0	6	125583	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.656	115	137	0.842	0.00000659	1709
Missense in Polyphen		33	39.12	0.84355		484
Synonymous	0.158	48	49.4	0.971	0.00000254	468
Loss of Function	1.92	5	12.3	0.408	6.02e-7	144

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the targeting and/or fusion of transport vesicles to their target membrane during transport of proteins from the early endosome to the lysosome. Required for heterotypic fusion of late endosomes with lysosomes and homotypic lysosomal fusion. Required for calcium regulated lysosomal exocytosis. Involved in the export of chylomicrons from the endoplasmic reticulum to the cis Golgi. Required for exocytosis of mediators during eosinophil and neutrophil degranulation, and target cell killing by natural killer cells. Required for focal exocytosis of late endocytic vesicles during phagosome formation. {ECO:0000269|PubMed:10888671, ECO:0000269|PubMed:16677249, ECO:0000269|PubMed:18042464}.
• Pathway: SNARE interactions in vesicular transport - Homo sapiens (human);Golgi Associated Vesicle Biogenesis;Lysosome Vesicle Biogenesis;Clathrin derived vesicle budding;Interleukin-12 family signaling;trans-Golgi Network Vesicle Budding;Signaling by Interleukins;Vesicle-mediated transport;Membrane Trafficking;Cytokine Signaling in Immune system;Immune System;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis;Interleukin-12 signaling (Consensus)

Recessive Scores

• pRec: 0.0934

Intolerance Scores

• loftool: 0.829
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.32

Haploinsufficiency Scores

• pHI: 0.221
• hipred: N
• hipred_score: 0.292
• ghis: 0.564

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.353

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Vamp7
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: exocytosis;endoplasmic reticulum to Golgi vesicle-mediated transport;vesicle fusion;phagocytosis, engulfment;endosome to lysosome transport;vesicle-mediated transport;calcium ion regulated exocytosis;triglyceride transport;SNARE complex assembly;Golgi to plasma membrane protein transport;eosinophil degranulation;neutrophil degranulation;natural killer cell degranulation;vesicle transport along microtubule;vesicle fusion with Golgi apparatus;positive regulation of dendrite morphogenesis;membrane organization;autophagosome maturation;regulation of protein targeting to vacuolar membrane;positive regulation of histamine secretion by mast cell
• Cellular component: cytoplasm;lysosomal membrane;endoplasmic reticulum membrane;trans-Golgi network;plasma membrane;cell surface;membrane;lamellipodium;cell junction;secretory granule;integral component of synaptic vesicle membrane;clathrin-coated vesicle membrane;secretory granule membrane;phagocytic vesicle membrane;platelet alpha granule;pseudopodium;SNARE complex;late endosome membrane;azurophil granule membrane;neuron projection;intracellular membrane-bounded organelle;apical part of cell;phagocytic vesicle;perinuclear region of cytoplasm;extracellular exosome;hippocampal mossy fiber to CA3 synapse
• Molecular function: SNARE binding;SNAP receptor activity;protein binding;syntaxin binding