USP34
Basic information
Region (hg38): 2:61187463-61471087
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 19 | ||||
missense | 247 | 251 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 2 | 1 | 3 | |||
non coding | 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:
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:
- 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