VAMP4

vesicle associated membrane protein 4, the group of Vesicle associated membrane proteins

Basic information

Region (hg38): 1:171700159-171742074

Links

ENSG00000117533 ∙ NCBI:8674 ∙ OMIM:606909 ∙ HGNC:12645 ∙ Uniprot:O75379 ∙ 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 VAMP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VAMP4 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						0
missense			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in VAMP4

This is a list of pathogenic ClinVar variants found in the VAMP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-171704528-A-G		not specified	Uncertain significance (Aug 08, 2023)
1-171704529-T-C		not specified	Uncertain significance (Jan 16, 2024)
1-171706406-T-C		not specified	Uncertain significance (Dec 01, 2022)
1-171709706-A-C		not specified	Uncertain significance (Aug 12, 2021)
1-171738372-T-A		not specified	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VAMP4	protein_coding	protein_coding	ENST00000236192	7	42088

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.144	0.839	125741	0	4	125745	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.680	57	73.4	0.777	0.00000367	936
Missense in Polyphen		9	14.977	0.60091		237
Synonymous	1.42	14	22.6	0.619	0.00000105	239
Loss of Function	2.06	3	10.1	0.298	4.91e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000339	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the pathway that functions to remove an inhibitor (probably synaptotagmin-4) of calcium-triggered exocytosis during the maturation of secretory granules. May be a marker for this sorting pathway that is critical for remodeling the secretory response of granule.
• Pathway: SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics;Vesicle-mediated transport;Membrane Trafficking;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.124

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.767
• hipred: Y
• hipred_score: 0.825
• ghis: 0.648

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.970

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vamp4

Gene ontology

• Biological process: microtubule cytoskeleton organization;endoplasmic reticulum to Golgi vesicle-mediated transport;synaptic vesicle to endosome fusion;SNARE complex assembly;Golgi to plasma membrane protein transport;membrane organization;Golgi ribbon formation;regulation of synaptic vesicle endocytosis
• Cellular component: Golgi membrane;lysosome;endosome;Golgi apparatus;plasma membrane;cell surface;transport vesicle;integral component of synaptic vesicle membrane;clathrin-coated vesicle membrane;trans-Golgi network membrane
• Molecular function: protein binding