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.

• not_specified (143 variants)
• not_provided (5 variants)
• Congenital_heart_disease (1 variants)

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. These statistics are base on transcript: NM_000153210.5. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	2	3
missense			128	15	1	144
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	128	16	3

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