USP34

ubiquitin specific peptidase 34, the group of Ubiquitin specific peptidases|Armadillo like helical domain containing|Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 2:61187463-61471087

Links

ENSG00000115464 ∙ NCBI:9736 ∙ OMIM:615295 ∙ HGNC:20066 ∙ Uniprot:Q70CQ2 ∙ 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 USP34 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the USP34 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				14	5	19
missense			247	1	3	251
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding			1			1
Total	0	0	248	15	8

Variants in USP34

This is a list of pathogenic ClinVar variants found in the USP34 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-61188143-C-T		not specified	Uncertain significance (Aug 26, 2024)
2-61188149-G-C		not specified	Uncertain significance (Jan 24, 2024)
2-61188176-G-A			Likely benign (Jul 18, 2018)
2-61188178-G-A		not specified	Uncertain significance (Mar 29, 2023)
2-61188185-A-C		not specified	Uncertain significance (Oct 24, 2024)
2-61188193-T-C		not specified	Uncertain significance (Nov 28, 2024)
2-61188212-A-G		not specified	Uncertain significance (Nov 09, 2021)
2-61188221-T-C		not specified	Uncertain significance (Mar 22, 2022)
2-61188262-T-C		not specified	Uncertain significance (Jul 06, 2021)
2-61188274-G-C		not specified	Uncertain significance (Jan 09, 2024)
2-61188284-C-G			Benign (May 14, 2018)
2-61188331-G-C		not specified	Uncertain significance (Aug 19, 2023)
2-61188332-T-C		not specified	Uncertain significance (Aug 19, 2024)
2-61188356-C-T		not specified	Uncertain significance (Oct 12, 2021)
2-61188357-A-G			Benign (May 01, 2021)
2-61188367-G-C		not specified	Uncertain significance (May 07, 2024)
2-61188379-C-G		not specified	Uncertain significance (Mar 19, 2024)
2-61188386-G-A		not specified	Uncertain significance (Sep 11, 2024)
2-61188398-C-G		not specified	Uncertain significance (Jan 23, 2024)
2-61188403-C-T		not specified	Uncertain significance (May 27, 2022)
2-61188431-G-T		not specified	Uncertain significance (Oct 08, 2024)
2-61188457-T-A		not specified	Uncertain significance (Sep 27, 2021)
2-61188457-T-C		not specified	Uncertain significance (May 15, 2024)
2-61188649-A-G		not specified	Uncertain significance (Aug 28, 2023)
2-61188653-T-G		not specified	Uncertain significance (Sep 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
USP34	protein_coding	protein_coding	ENST00000398571	80	283307

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	4.13e-25	124757	0	28	124785	0.000112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.34	1513	1.79e+3	0.844	0.0000905	23551
Missense in Polyphen		255	517.94	0.49233		7045
Synonymous	-5.27	784	617	1.27	0.0000318	6361
Loss of Function	12.4	11	200	0.0550	0.0000109	2470

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000159	0.000159
Ashkenazi Jewish	0.00	0.00
East Asian	0.000350	0.000334
Finnish	0.00	0.00
European (Non-Finnish)	0.000153	0.000150
Middle Eastern	0.000350	0.000334
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ubiquitin hydrolase that can remove conjugated ubiquitin from AXIN1 and AXIN2, thereby acting as a regulator of Wnt signaling pathway. Acts as an activator of the Wnt signaling pathway downstream of the beta-catenin destruction complex by deubiquitinating and stabilizing AXIN1 and AXIN2, leading to promote nuclear accumulation of AXIN1 and AXIN2 and positively regulate beta-catenin (CTNBB1)-mediated transcription. Recognizes and hydrolyzes 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. {ECO:0000269|PubMed:21383061}.
• Pathway: Signaling by WNT;Signal Transduction;Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination;TCF dependent signaling in response to WNT (Consensus)

Recessive Scores

• pRec: 0.0952

Intolerance Scores

• loftool: 0.111
• rvis_EVS: -3.59
• rvis_percentile_EVS: 0.3

Haploinsufficiency Scores

• pHI: 0.838
• hipred: Y
• hipred_score: 0.554
• ghis: 0.672

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.777

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Usp34
• Phenotype: homeostasis/metabolism phenotype; skeleton phenotype

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;Wnt signaling pathway;protein deubiquitination;regulation of protein stability;protein K48-linked deubiquitination;positive regulation of canonical Wnt signaling pathway
• Cellular component: cytosol
• Molecular function: cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;protein binding;thiol-dependent ubiquitinyl hydrolase activity