USP12

ubiquitin specific peptidase 12, the group of Ubiquitin specific peptidases

Basic information

Region (hg38): 13:27066156-27171811

Previous symbols: [ "USP12L1" ]

Links

ENSG00000152484

∙ NCBI:219333 ∙ OMIM:603091 ∙ HGNC:20485 ∙ Uniprot:O75317 ∙ 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 USP12 gene.

not_specified (24 variants)

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. These statistics are base on transcript: NM_000182488.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	1 clinvar		4
missense			24 clinvar			24
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	30	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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