USP43

ubiquitin specific peptidase 43, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 17:9644698-9729687

Links

ENSG00000154914 ∙ NCBI:124739 ∙ ∙ HGNC:20072 ∙ Uniprot:Q70EL4 ∙ 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 USP43 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP43 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				1	2	3
missense			84	10	1	95
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	84	11	3

Variants in USP43

This is a list of pathogenic ClinVar variants found in the USP43 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-9645655-C-G		not specified	Uncertain significance (Sep 25, 2024)
17-9645670-C-A		not specified	Uncertain significance (Aug 02, 2021)
17-9645670-C-T		not specified	Uncertain significance (May 14, 2024)
17-9645684-C-T		not specified	Uncertain significance (May 14, 2024)
17-9645688-G-A		not specified	Uncertain significance (Aug 05, 2024)
17-9645688-G-T		not specified	Uncertain significance (Nov 29, 2024)
17-9645690-C-G		not specified	Uncertain significance (Feb 27, 2024)
17-9645694-G-C		not specified	Uncertain significance (Jan 03, 2024)
17-9645720-C-G		not specified	Uncertain significance (May 11, 2022)
17-9645720-C-T		not specified	Uncertain significance (Jan 04, 2022)
17-9645733-C-A		not specified	Uncertain significance (Dec 03, 2024)
17-9645744-C-G		not specified	Uncertain significance (Nov 23, 2022)
17-9645756-G-A		not specified	Uncertain significance (Jan 23, 2023)
17-9645788-C-A		not specified	Uncertain significance (Sep 09, 2024)
17-9645810-G-A		not specified	Uncertain significance (Aug 02, 2021)
17-9645868-G-A		not specified	Uncertain significance (Jul 05, 2023)
17-9645880-C-A		not specified	Uncertain significance (Dec 06, 2024)
17-9645916-C-T		not specified	Uncertain significance (Oct 05, 2021)
17-9646042-C-T		not specified	Uncertain significance (Apr 07, 2023)
17-9646070-G-T		not specified	Uncertain significance (Sep 06, 2022)
17-9646131-T-C		not specified	Uncertain significance (Jan 30, 2024)
17-9656439-A-G		not specified	Uncertain significance (Nov 30, 2021)
17-9656505-G-A		not specified	Uncertain significance (Oct 17, 2023)
17-9656521-C-T		not specified	Uncertain significance (Sep 27, 2024)
17-9666745-A-T		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP43	protein_coding	protein_coding	ENST00000285199	15	84994

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.164	0.836	124631	0	27	124658	0.000108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.58	468	575	0.814	0.0000329	7149
Missense in Polyphen		76	156.04	0.48706		2055
Synonymous	1.65	209	242	0.865	0.0000144	2355
Loss of Function	4.76	11	45.7	0.241	0.00000257	516

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000449	0.000445
Finnish	0.00	0.00
European (Non-Finnish)	0.000107	0.0000973
Middle Eastern	0.000449	0.000445
South Asian	0.0000983	0.0000980
Other	0.000167	0.000165

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: DNA Repair;Termination of translesion DNA synthesis;Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template;DNA Damage Bypass (Consensus)

Recessive Scores

• pRec: 0.0941

Intolerance Scores

• loftool: 0.688
• rvis_EVS: -0.81
• rvis_percentile_EVS: 12.05

Haploinsufficiency Scores

• pHI: 0.0739
• hipred: N
• hipred_score: 0.476
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.675

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp43

Zebrafish Information Network

• Gene name: usp43a
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: curled

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein deubiquitination;translesion synthesis
• Cellular component: nucleoplasm
• Molecular function: ISG15-specific protease activity;thiol-dependent ubiquitinyl hydrolase activity