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

ENSG00000115464NCBI:9736OMIM:615295HGNC:20066Uniprot:Q70CQ2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
5
clinvar
19
missense
247
clinvar
1
clinvar
3
clinvar
251
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
2
1
3
non coding
1
clinvar
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)3466907
2-61188149-G-C not specified Uncertain significance (Jan 24, 2024)3187439
2-61188176-G-A Likely benign (Jul 18, 2018)723882
2-61188178-G-A not specified Uncertain significance (Mar 29, 2023)2530998
2-61188185-A-C not specified Uncertain significance (Oct 24, 2024)3466952
2-61188193-T-C not specified Uncertain significance (Nov 28, 2024)3466950
2-61188212-A-G not specified Uncertain significance (Nov 09, 2021)2259970
2-61188221-T-C not specified Uncertain significance (Mar 22, 2022)2279369
2-61188262-T-C not specified Uncertain significance (Jul 06, 2021)2229017
2-61188274-G-C not specified Uncertain significance (Jan 09, 2024)3187438
2-61188284-C-G Benign (May 14, 2018)712266
2-61188331-G-C not specified Uncertain significance (Aug 19, 2023)2602511
2-61188332-T-C not specified Uncertain significance (Aug 19, 2024)3466913
2-61188356-C-T not specified Uncertain significance (Oct 12, 2021)2255182
2-61188357-A-G Benign (May 01, 2021)1229915
2-61188367-G-C not specified Uncertain significance (May 07, 2024)3331496
2-61188379-C-G not specified Uncertain significance (Mar 19, 2024)3331471
2-61188386-G-A not specified Uncertain significance (Sep 11, 2024)3466945
2-61188398-C-G not specified Uncertain significance (Jan 23, 2024)3187437
2-61188403-C-T not specified Uncertain significance (May 27, 2022)2384986
2-61188431-G-T not specified Uncertain significance (Oct 08, 2024)3466949
2-61188457-T-A not specified Uncertain significance (Sep 27, 2021)2252329
2-61188457-T-C not specified Uncertain significance (May 15, 2024)3331479
2-61188649-A-G not specified Uncertain significance (Aug 28, 2023)2622225
2-61188653-T-G not specified Uncertain significance (Sep 26, 2024)3466947

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
USP34protein_codingprotein_codingENST00000398571 80283307
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.004.13e-251247570281247850.000112
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.3415131.79e+30.8440.000090523551
Missense in Polyphen255517.940.492337045
Synonymous-5.277846171.270.00003186361
Loss of Function12.4112000.05500.00001092470

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001590.000159
Ashkenazi Jewish0.000.00
East Asian0.0003500.000334
Finnish0.000.00
European (Non-Finnish)0.0001530.000150
Middle Eastern0.0003500.000334
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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