MVP

major vault protein

Basic information

Region (hg38): 16:29820394-29848039

Links

ENSG00000013364 ∙ NCBI:9961 ∙ OMIM:605088 ∙ HGNC:7531 ∙ Uniprot:Q14764 ∙ 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 MVP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MVP 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				4	1	5
missense			53	4	3	60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	53	8	4

Variants in MVP

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

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

Position	Type	Phenotype	Significance	ClinVar
16-29830589-C-T		not specified	Uncertain significance (Mar 30, 2024)
16-29830629-G-A			Benign (Mar 29, 2018)
16-29830659-G-A		not specified	Uncertain significance (Jun 28, 2023)
16-29830897-C-T		not specified	Uncertain significance (Oct 29, 2021)
16-29830898-G-A		not specified	Uncertain significance (Jul 09, 2024)
16-29830906-A-T		not specified	Uncertain significance (Sep 03, 2024)
16-29830909-G-A			Likely benign (May 16, 2018)
16-29830919-G-A		not specified	Uncertain significance (Jul 19, 2023)
16-29830949-C-G		not specified	Uncertain significance (Nov 12, 2024)
16-29830952-G-A		not specified	Uncertain significance (Jan 08, 2024)
16-29830993-G-T		not specified	Uncertain significance (May 29, 2024)
16-29830997-G-A		not specified	Uncertain significance (Aug 02, 2022)
16-29831057-G-A		not specified	Uncertain significance (Dec 20, 2023)
16-29833749-A-G		not specified	Uncertain significance (Jul 02, 2024)
16-29833766-A-T		not specified	Uncertain significance (Mar 08, 2024)
16-29833824-T-A		not specified	Uncertain significance (Dec 19, 2022)
16-29833846-C-T			Likely benign (Jul 01, 2022)
16-29833943-A-C		not specified	Uncertain significance (May 23, 2023)
16-29833950-G-A		not specified	Likely benign (Aug 17, 2021)
16-29834013-G-T		not specified	Uncertain significance (Jan 03, 2024)
16-29834034-G-T		not specified	Uncertain significance (Dec 27, 2022)
16-29834060-G-A		not specified	Uncertain significance (Dec 17, 2023)
16-29835725-C-G		not specified	Uncertain significance (Dec 14, 2023)
16-29835746-C-T		not specified	Uncertain significance (Jul 30, 2024)
16-29835772-G-A		not specified	Uncertain significance (Nov 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MVP	protein_coding	protein_coding	ENST00000357402	14	27641

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.76e-8	0.999	125603	0	145	125748	0.000577

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.02	431	566	0.762	0.0000376	5684
Missense in Polyphen		227	298.44	0.76061		2953
Synonymous	0.564	235	246	0.954	0.0000162	1915
Loss of Function	2.87	18	36.8	0.489	0.00000183	412

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000814	0.000809
Ashkenazi Jewish	0.000300	0.000298
East Asian	0.000109	0.000109
Finnish	0.00185	0.00157
European (Non-Finnish)	0.000653	0.000633
Middle Eastern	0.000109	0.000109
South Asian	0.000362	0.000359
Other	0.000492	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for normal vault structure. Vaults are multi- subunit structures that may act as scaffolds for proteins involved in signal transduction. Vaults may also play a role in nucleo- cytoplasmic transport. Down-regulates IFNG-mediated STAT1 signaling and subsequent activation of JAK. Down-regulates SRC activity and signaling through MAP kinases. {ECO:0000269|PubMed:15133037, ECO:0000269|PubMed:16418217, ECO:0000269|PubMed:16441665}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.219

Intolerance Scores

• loftool: 0.797
• rvis_EVS: -0.81
• rvis_percentile_EVS: 12.05

Haploinsufficiency Scores

• pHI: 0.129
• hipred: Y
• hipred_score: 0.520
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.992

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mvp
• Phenotype: normal phenotype

Zebrafish Information Network

• Gene name: mvp
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: protein transport;negative regulation of signaling;negative regulation of protein autophosphorylation;ERBB signaling pathway;neutrophil degranulation;mRNA transport;negative regulation of protein tyrosine kinase activity
• Cellular component: extracellular region;nucleus;nuclear pore;cytoplasm;cytosol;cytoskeleton;membrane;secretory granule lumen;perinuclear region of cytoplasm;extracellular exosome;ficolin-1-rich granule lumen
• Molecular function: protein binding;protein kinase binding;protein phosphatase binding;identical protein binding