USP29

ubiquitin specific peptidase 29, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 19:57119137-57131926

Links

ENSG00000131864 ∙ NCBI:57663 ∙ OMIM:609546 ∙ HGNC:18563 ∙ Uniprot:Q9HBJ7 ∙ 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 USP29 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP29 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	1	2
missense			49	5		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	6	1

Variants in USP29

This is a list of pathogenic ClinVar variants found in the USP29 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57128680-T-C		not specified	Uncertain significance (Jan 11, 2023)
19-57128722-A-G		not specified	Likely benign (Apr 09, 2024)
19-57128793-G-A		not specified	Uncertain significance (Mar 16, 2023)
19-57128808-G-A		not specified	Uncertain significance (Nov 07, 2022)
19-57128817-A-G		not specified	Uncertain significance (Dec 15, 2022)
19-57128842-A-T		not specified	Uncertain significance (Aug 08, 2023)
19-57129013-C-A		not specified	Uncertain significance (Feb 01, 2023)
19-57129183-C-A		not specified	Likely benign (Mar 25, 2024)
19-57129211-C-G		not specified	Uncertain significance (Sep 29, 2023)
19-57129220-A-G		not specified	Uncertain significance (Apr 05, 2023)
19-57129222-A-C		not specified	Uncertain significance (Apr 24, 2024)
19-57129225-C-G		not specified	Uncertain significance (Mar 24, 2023)
19-57129268-A-T		not specified	Uncertain significance (Jun 05, 2023)
19-57129280-A-G		not specified	Uncertain significance (Mar 28, 2024)
19-57129296-G-A			Benign (May 18, 2018)
19-57129318-G-A		not specified	Uncertain significance (May 06, 2024)
19-57129485-C-G		not specified	Uncertain significance (Dec 15, 2023)
19-57129619-C-T		not specified	Uncertain significance (Jan 24, 2024)
19-57129636-G-A		not specified	Uncertain significance (Sep 07, 2022)
19-57129706-C-A		not specified	Uncertain significance (Jul 12, 2022)
19-57129741-A-G		not specified	Uncertain significance (Sep 15, 2021)
19-57129764-A-T		not specified	Uncertain significance (Dec 16, 2023)
19-57129795-C-T		not specified	Uncertain significance (May 06, 2022)
19-57129807-G-A		not specified	Uncertain significance (Mar 20, 2024)
19-57129851-T-G		not specified	Uncertain significance (Dec 15, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP29	protein_coding	protein_coding	ENST00000254181	1	12789

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0823	460	465	0.989	0.0000213	6157
Missense in Polyphen		87	103.9	0.83735		1487
Synonymous	0.0686	176	177	0.993	0.00000863	1711
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0718

Intolerance Scores

• loftool: 0.743
• rvis_EVS: 1.67
• rvis_percentile_EVS: 96.33

Haploinsufficiency Scores

• pHI: 0.0762
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.565

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp29

Gene ontology

• Biological process: G1/S transition of mitotic cell cycle;ubiquitin-dependent protein catabolic process;protein deubiquitination
• Cellular component: cellular_component;nucleus
• Molecular function: cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;thiol-dependent ubiquitinyl hydrolase activity