USP12
Basic information
Region (hg38): 13:27066156-27171811
Previous symbols: [ "USP12L1" ]
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 USP12 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 | |||||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 1 | 0 |
Variants in USP12
This is a list of pathogenic ClinVar variants found in the USP12 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 13-27069358-T-G | not specified | Uncertain significance (Jan 23, 2024) | ||
| 13-27069377-T-C | not specified | Uncertain significance (Dec 20, 2024) | ||
| 13-27075252-C-G | not specified | Uncertain significance (Jul 14, 2024) | ||
| 13-27075282-G-A | not specified | Uncertain significance (Jan 29, 2024) | ||
| 13-27075368-G-C | not specified | Uncertain significance (Oct 12, 2024) | ||
| 13-27095644-T-C | not specified | Uncertain significance (Jun 27, 2023) | ||
| 13-27095668-G-C | not specified | Uncertain significance (Jul 25, 2023) | ||
| 13-27105761-T-C | not specified | Uncertain significance (Aug 13, 2021) | ||
| 13-27105829-G-T | not specified | Uncertain significance (Dec 27, 2023) | ||
| 13-27116571-T-C | not specified | Uncertain significance (Sep 20, 2023) | ||
| 13-27116582-C-T | not specified | Likely benign (Aug 19, 2024) | ||
| 13-27116593-C-T | not specified | Uncertain significance (Nov 24, 2024) | ||
| 13-27171609-C-A | not specified | Uncertain significance (Jan 19, 2025) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| USP12 | protein_coding | protein_coding | ENST00000282344 | 9 | 105741 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.971 | 0.0295 | 125650 | 0 | 6 | 125656 | 0.0000239 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.82 | 90 | 203 | 0.443 | 0.0000110 | 2465 |
| Missense in Polyphen | 4 | 64.323 | 0.062186 | 868 | ||
| Synonymous | 0.629 | 63 | 69.7 | 0.904 | 0.00000376 | 655 |
| Loss of Function | 3.70 | 2 | 19.7 | 0.101 | 9.63e-7 | 258 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000616 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000265 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000392 | 0.0000327 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Deubiquitinating enzyme. Has almost no deubiquitinating activity by itself and requires the interaction with WDR20 and WDR48 to have a high activity (PubMed:19075014, PubMed:27373336). Not involved in deubiquitination of monoubiquitinated FANCD2 (PubMed:19075014). In complex with WDR48, acts as a potential tumor suppressor by positively regulating PHLPP1 stability (PubMed:24145035). {ECO:0000269|PubMed:19075014, ECO:0000269|PubMed:24145035, ECO:0000269|PubMed:27373336}.;
- Pathway
- Post-translational protein modification;Metabolism of proteins;Ub-specific processing proteases;Deubiquitination
(Consensus)
Intolerance Scores
- loftool
- 0.441
- rvis_EVS
- -0.1
- rvis_percentile_EVS
- 46.49
Haploinsufficiency Scores
- pHI
- 0.403
- hipred
- Y
- hipred_score
- 0.796
- ghis
- 0.554
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.881
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Usp12
- Phenotype
- immune system phenotype; limbs/digits/tail phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- usp12b
- Affected structure
- post-vent region
- Phenotype tag
- abnormal
- Phenotype quality
- necrotic
Gene ontology
- Biological process
- ubiquitin-dependent protein catabolic process;protein deubiquitination
- Cellular component
- cellular_component;nucleoplasm
- Molecular function
- cysteine-type endopeptidase activity;thiol-dependent ubiquitin-specific protease activity;protein binding;thiol-dependent ubiquitinyl hydrolase activity;metal ion binding