VCPIP1

valosin containing protein interacting protein 1, the group of OTU domain containing

Basic information

Region (hg38): 8:66628487-66667231

Links

ENSG00000175073 ∙ NCBI:80124 ∙ OMIM:611745 ∙ HGNC:30897 ∙ Uniprot:Q96JH7 ∙ 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 VCPIP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VCPIP1 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			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	1	0

Variants in VCPIP1

This is a list of pathogenic ClinVar variants found in the VCPIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-66634625-G-A		not specified	Uncertain significance (Jun 04, 2024)
8-66634631-G-A		not specified	Uncertain significance (Apr 09, 2024)
8-66634664-T-A		not specified	Uncertain significance (Mar 24, 2023)
8-66634719-C-G		not specified	Uncertain significance (Apr 23, 2024)
8-66634736-C-T		not specified	Uncertain significance (Apr 01, 2024)
8-66634754-C-T		not specified	Uncertain significance (Aug 22, 2023)
8-66634796-C-T		not specified	Uncertain significance (Dec 02, 2021)
8-66634807-G-C		not specified	Uncertain significance (Jan 02, 2024)
8-66634913-G-A		not specified	Uncertain significance (Dec 20, 2023)
8-66634941-T-C		not specified	Uncertain significance (Jan 17, 2024)
8-66634980-A-T		not specified	Uncertain significance (May 03, 2024)
8-66635055-G-T		not specified	Uncertain significance (Jun 11, 2024)
8-66635208-C-T		not specified	Uncertain significance (Nov 17, 2022)
8-66635324-G-T		not specified	Uncertain significance (Jan 19, 2024)
8-66651463-G-T		not specified	Uncertain significance (Mar 19, 2024)
8-66651544-C-T		not specified	Uncertain significance (May 26, 2024)
8-66664449-G-C		not specified	Uncertain significance (Sep 17, 2021)
8-66664533-T-C		not specified	Uncertain significance (Jan 10, 2023)
8-66664542-C-G		not specified	Uncertain significance (May 02, 2024)
8-66664648-T-G		not specified	Uncertain significance (May 15, 2024)
8-66664663-G-A		not specified	Uncertain significance (Dec 18, 2023)
8-66664674-G-T		not specified	Uncertain significance (Dec 11, 2023)
8-66664717-G-A		not specified	Uncertain significance (Mar 31, 2024)
8-66664749-T-C		not specified	Uncertain significance (May 25, 2022)
8-66664943-G-T		not specified	Uncertain significance (Mar 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VCPIP1	protein_coding	protein_coding	ENST00000310421	3	38731

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000305	125740	0	6	125746	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.56	391	645	0.606	0.0000306	7990
Missense in Polyphen		62	212.26	0.29209		2643
Synonymous	0.0931	241	243	0.992	0.0000116	2491
Loss of Function	5.71	1	39.9	0.0250	0.00000237	492

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a deubiquitinating enzyme. Necessary for VCP- mediated reassembly of Golgi stacks after mitosis. May play a role in VCP-mediated formation of transitional endoplasmic reticulum (tER). Mediates dissociation of the ternary complex containing STX5A, NSFL1C and VCP (By similarity). Hydrolyzes 'Lys-11'- and 'Lys-48'-linked polyubiquitin chains. {ECO:0000250, ECO:0000269|PubMed:23827681}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Ovarian tumor domain proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.0703
• rvis_EVS: -0.84
• rvis_percentile_EVS: 11.28

Haploinsufficiency Scores

• pHI: 0.242
• hipred: Y
• hipred_score: 0.765
• ghis: 0.561

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.954

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Vcpip1

Zebrafish Information Network

• Gene name: vcpip1
• Affected structure: caudal fin upper lobe
• Phenotype tag: abnormal
• Phenotype quality: fused with

Gene ontology

• Biological process: mitotic cell cycle;endoplasmic reticulum membrane fusion;protein ubiquitination;protein K11-linked deubiquitination;protein K48-linked deubiquitination;Golgi reassembly
• Cellular component: cytoplasm;endoplasmic reticulum lumen;Golgi stack
• Molecular function: thiol-dependent ubiquitin-specific protease activity