SVIP

small VCP interacting protein

Basic information

Region (hg38): 11:22813799-22830299

Links

ENSG00000198168 ∙ NCBI:258010 ∙ ∙ HGNC:25238 ∙ Uniprot:Q8NHG7 ∙ 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 SVIP gene.

Variants pathogenicity by type

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

Variants in SVIP

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

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

Position	Type	Phenotype	Significance	ClinVar
11-22827273-T-A		not specified	Uncertain significance (Jul 21, 2021)
11-22827861-G-C		not specified	Uncertain significance (Apr 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SVIP	protein_coding	protein_coding	ENST00000354193	4	16501

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000300	0.365	124728	0	61	124789	0.000244

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.444	30	37.7	0.797	0.00000186	469
Missense in Polyphen		14	18.226	0.76812		231
Synonymous	0.680	10	13.1	0.761	5.78e-7	149
Loss of Function	-0.170	5	4.61	1.09	1.93e-7	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000785	0.000749
Ashkenazi Jewish	0.00	0.00
East Asian	0.000372	0.000334
Finnish	0.00	0.00
European (Non-Finnish)	0.000262	0.000247
Middle Eastern	0.000372	0.000334
South Asian	0.000310	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Protein processing in endoplasmic reticulum - Homo sapiens (human);Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Intolerance Scores

• loftool: 0.680
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.493
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Svip

Gene ontology

• Biological process: positive regulation of autophagy;negative regulation of protein complex assembly;neutrophil degranulation;positive regulation of protein lipidation;negative regulation of ER-associated ubiquitin-dependent protein catabolic process;negative regulation of retrograde protein transport, ER to cytosol;negative regulation of VCP-NPL4-UFD1 AAA ATPase complex assembly
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;plasma membrane;secretory granule membrane;smooth endoplasmic reticulum membrane;anchored component of membrane;extracellular exosome;tertiary granule membrane
• Molecular function: protein binding;protein self-association;ATPase binding