USP31

ubiquitin specific peptidase 31, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 16:23061406-23149452

Links

ENSG00000103404 ∙ NCBI:57478 ∙ OMIM:619536 ∙ HGNC:20060 ∙ Uniprot:Q70CQ4 ∙ 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 USP31 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP31 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				2		2
missense			87	3		90
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	87	5	0

Variants in USP31

This is a list of pathogenic ClinVar variants found in the USP31 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-23068087-T-C			Likely benign (Apr 01, 2023)
16-23068102-T-C		not specified	Uncertain significance (Oct 20, 2024)
16-23068134-G-A		not specified	Uncertain significance (Mar 06, 2023)
16-23068153-A-T		not specified	Uncertain significance (Jan 26, 2022)
16-23068167-G-A		not specified	Uncertain significance (Nov 08, 2022)
16-23068179-C-A		not specified	Uncertain significance (Aug 26, 2024)
16-23068272-G-A		not specified	Uncertain significance (Sep 02, 2024)
16-23068360-A-T		not specified	Uncertain significance (Oct 21, 2024)
16-23068383-G-A		not specified	Uncertain significance (Nov 28, 2023)
16-23068386-C-T		not specified	Uncertain significance (Dec 11, 2023)
16-23068387-G-A		not specified	Uncertain significance (Jul 26, 2022)
16-23068390-G-A		not specified	Uncertain significance (Feb 13, 2024)
16-23068480-T-C		not specified	Likely benign (Nov 15, 2024)
16-23068491-C-T		not specified	Uncertain significance (May 09, 2023)
16-23068492-G-A		not specified	Uncertain significance (Dec 22, 2023)
16-23068519-C-T		not specified	Uncertain significance (Oct 27, 2023)
16-23068528-C-T		not specified	Uncertain significance (May 28, 2024)
16-23068557-T-C		not specified	Uncertain significance (Jul 17, 2024)
16-23068566-C-T		not specified	Uncertain significance (Aug 10, 2021)
16-23068570-G-C		not specified	Uncertain significance (Jan 23, 2023)
16-23068579-G-A		not specified	Uncertain significance (Dec 08, 2021)
16-23068591-A-T		not specified	Uncertain significance (Dec 21, 2022)
16-23068594-T-C		not specified	Uncertain significance (Dec 21, 2022)
16-23068654-C-T		not specified	Uncertain significance (Oct 26, 2022)
16-23068704-G-A		not specified	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP31	protein_coding	protein_coding	ENST00000219689	16	87865

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0621	0.938	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	595	705	0.844	0.0000404	8697
Missense in Polyphen		210	318.9	0.65852		3799
Synonymous	-1.56	319	286	1.12	0.0000171	2796
Loss of Function	4.98	13	51.6	0.252	0.00000260	642

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000182	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.000326	0.000326
South Asian	0.0000654	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May recognize and hydrolyze the peptide bond at the C- terminal Gly of ubiquitin. Involved in the processing of poly- ubiquitin precursors as well as that of ubiquitinated proteins (By similarity). {ECO:0000250}.
• Pathway: EGFR1 (Consensus)

Intolerance Scores

• loftool: 0.570
• rvis_EVS: -0.06
• rvis_percentile_EVS: 48.91

Haploinsufficiency Scores

• pHI: 0.332
• hipred: Y
• hipred_score: 0.639
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.945

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp31

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein deubiquitination
• Cellular component: nucleus
• Molecular function: thiol-dependent ubiquitin-specific protease activity