USP1

ubiquitin specific peptidase 1, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 1:62436297-62451804

Links

ENSG00000162607 ∙ NCBI:7398 ∙ OMIM:603478 ∙ HGNC:12607 ∙ Uniprot:O94782 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the USP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP1 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			35	1		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	1	2

Variants in USP1

This is a list of pathogenic ClinVar variants found in the USP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-62441492-C-A		not specified	Uncertain significance (Aug 02, 2021)
1-62441543-A-G		not specified	Uncertain significance (Aug 19, 2023)
1-62442213-G-A		not specified	Uncertain significance (May 12, 2024)
1-62443178-C-T		not specified	Uncertain significance (May 17, 2023)
1-62443204-A-G		not specified	Uncertain significance (Aug 22, 2023)
1-62443268-A-G		not specified	Uncertain significance (Jul 13, 2021)
1-62444896-C-T		not specified	Uncertain significance (Feb 09, 2023)
1-62444916-A-G		not specified	Uncertain significance (Oct 12, 2021)
1-62444941-T-G		not specified	Uncertain significance (Dec 19, 2023)
1-62444965-A-C		not specified	Uncertain significance (Feb 06, 2023)
1-62445039-T-C		not specified	Uncertain significance (Jun 11, 2021)
1-62445065-G-T		not specified	Uncertain significance (Jul 09, 2024)
1-62445148-C-T		not specified	Uncertain significance (Nov 17, 2022)
1-62445165-A-G		not specified	Uncertain significance (Jul 14, 2021)
1-62445174-C-A		not specified	Uncertain significance (Feb 07, 2023)
1-62445195-A-G		not specified	Uncertain significance (Mar 01, 2023)
1-62445226-C-T		not specified	Uncertain significance (Aug 30, 2022)
1-62445230-C-T			Benign (Jun 21, 2018)
1-62445240-A-G		not specified	Uncertain significance (Dec 17, 2023)
1-62445272-C-G		not specified	Uncertain significance (Aug 30, 2022)
1-62445274-A-G		not specified	Uncertain significance (Dec 20, 2021)
1-62445275-A-C		not specified	Uncertain significance (Jun 18, 2021)
1-62445310-A-T		not specified	Uncertain significance (Mar 18, 2024)
1-62445348-A-G		not specified	Uncertain significance (Dec 06, 2022)
1-62445363-G-A		not specified	Uncertain significance (Jul 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP1	protein_coding	protein_coding	ENST00000339950	8	15508

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00309	125731	0	8	125739	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	321	379	0.847	0.0000171	5204
Missense in Polyphen		64	143.54	0.44588		2023
Synonymous	-0.738	148	137	1.08	0.00000668	1419
Loss of Function	4.59	3	30.2	0.0993	0.00000144	456

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000629	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Negative regulator of DNA damage repair which specifically deubiquitinates monoubiquitinated FANCD2 (PubMed:15694335). Also involved in PCNA-mediated translesion synthesis (TLS) by deubiquitinating monoubiquitinated PCNA (PubMed:16531995). Has almost no deubiquitinating activity by itself and requires the interaction with WDR48 to have a high activity (PubMed:18082604, PubMed:26388029). {ECO:0000269|PubMed:15694335, ECO:0000269|PubMed:16531995, ECO:0000269|PubMed:18082604, ECO:0000269|PubMed:26388029}.
• Pathway: Fanconi anemia pathway - Homo sapiens (human);miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-517 relationship with ARCN1 and USP1;Fanconi Anemia Pathway;DNA Repair;Fanconi anemia pathway;Recognition of DNA damage by PCNA-containing replication complex;DNA Damage Bypass (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.535
• rvis_EVS: -0.64
• rvis_percentile_EVS: 16.63

Haploinsufficiency Scores

• pHI: 0.302
• hipred: Y
• hipred_score: 0.783
• ghis: 0.670

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.898

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp1
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; growth/size/body region phenotype; skeleton phenotype

Zebrafish Information Network

• Gene name: usp1
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: curled

Gene ontology

• Biological process: skeletal system development;DNA repair;regulation of DNA repair;ubiquitin-dependent protein catabolic process;response to UV;protein deubiquitination;monoubiquitinated protein deubiquitination;DNA damage response, detection of DNA damage
• Cellular component: nucleus;nucleoplasm
• Molecular function: cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;protein binding;peptidase activity;thiol-dependent ubiquitinyl hydrolase activity