VAMP5

vesicle associated membrane protein 5, the group of Vesicle associated membrane proteins

Basic information

Region (hg38): 2:85584431-85593406

Links

ENSG00000168899 ∙ NCBI:10791 ∙ OMIM:607029 ∙ HGNC:12646 ∙ Uniprot:O95183 ∙ 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 VAMP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VAMP5 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			13	2		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	2	0

Variants in VAMP5

This is a list of pathogenic ClinVar variants found in the VAMP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-85591775-A-T		not specified	Uncertain significance (Dec 22, 2023)
2-85591776-A-C		not specified	Uncertain significance (Jul 13, 2021)
2-85591781-G-C		not specified	Uncertain significance (Oct 24, 2023)
2-85591782-C-T		not specified	Uncertain significance (Jan 24, 2024)
2-85591815-G-A		not specified	Uncertain significance (Aug 11, 2022)
2-85592989-G-C		not specified	Uncertain significance (Dec 13, 2023)
2-85593009-G-A		not specified	Uncertain significance (Feb 17, 2022)
2-85593015-G-A		not specified	Uncertain significance (Nov 17, 2022)
2-85593023-G-A		not specified	Uncertain significance (Mar 11, 2024)
2-85593029-C-A		not specified	Uncertain significance (Dec 26, 2023)
2-85593077-G-A		not specified	Likely benign (Jan 10, 2022)
2-85593110-G-A		not specified	Uncertain significance (Dec 14, 2023)
2-85593116-C-T		not specified	Uncertain significance (Sep 14, 2021)
2-85593117-G-A		not specified	Likely benign (Aug 02, 2023)
2-85593129-C-T		not specified	Uncertain significance (Nov 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VAMP5	protein_coding	protein_coding	ENST00000306384	3	9005

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0111	0.642	125587	0	157	125744	0.000624

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0798	73	74.9	0.974	0.00000503	750
Missense in Polyphen		22	29.386	0.74867		283
Synonymous	-0.650	34	29.5	1.15	0.00000175	243
Loss of Function	0.430	3	3.92	0.766	1.67e-7	50

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.0122	0.0123
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000202	0.000202
Middle Eastern	0.000217	0.000217
South Asian	0.00	0.00
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May participate in trafficking events that are associated with myogenesis, such as myoblast fusion and/or GLUT4 trafficking.
• Pathway: SNARE interactions in vesicular transport - Homo sapiens (human);Nicotine Pathway (Dopaminergic Neuron), Pharmacodynamics (Consensus)

Recessive Scores

• pRec: 0.0260

Intolerance Scores

• loftool: 0.527
• rvis_EVS: -0.14
• rvis_percentile_EVS: 42.88

Haploinsufficiency Scores

• pHI: 0.0106
• hipred: N
• hipred_score: 0.123
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.281

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vamp5
• Phenotype: growth/size/body region phenotype; renal/urinary system phenotype; respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: muscle organ development;skeletal muscle tissue development;cell differentiation;Golgi to plasma membrane protein transport
• Cellular component: late endosome;trans-Golgi network;plasma membrane;integral component of plasma membrane;cell surface;intercalated disc;cytoplasmic vesicle membrane;integral component of organelle membrane;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: protein binding