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.

not_specified (108 variants)
not_provided (10 variants)

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. These statistics are base on transcript: NM_000005115.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar	1 clinvar	6
missense			102 clinvar	6 clinvar	3 clinvar	111
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	102	11	4

Loading clinvar variants...

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