UBASH3B

ubiquitin associated and SH3 domain containing B, the group of Protein phosphatases

Basic information

Region (hg38): 11:122655722-122814473

Links

ENSG00000154127

∙ NCBI:84959 ∙ OMIM:609201 ∙ HGNC:29884 ∙ Uniprot:Q8TF42 ∙ 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 UBASH3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBASH3B gene is commonly pathogenic or not. These statistics are base on transcript: . 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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3 clinvar	3 clinvar	6
missense			37 clinvar	1 clinvar	1 clinvar	39
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	37	4	4

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBASH3B	protein_coding	protein_coding	ENST00000284273	14	158799

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000471	1.00	125728	0	19	125747	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	263	371	0.709	0.0000210	4217
Missense in Polyphen		91	152.4	0.5971		1741
Synonymous	1.38	129	151	0.857	0.00000938	1255
Loss of Function	3.47	14	36.6	0.382	0.00000192	403

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.000109	0.000109
South Asian	0.000232	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Interferes with CBL-mediated down-regulation and degradation of receptor-type tyrosine kinases. Promotes accumulation of activated target receptors, such as T-cell receptors and EGFR, on the cell surface. Exhibits tyrosine phosphatase activity toward several substrates including EGFR, FAK, SYK, and ZAP70. Down-regulates proteins that are dually modified by both protein tyrosine phosphorylation and ubiquitination. {ECO:0000269|PubMed:15159412, ECO:0000269|PubMed:17880946}.;
Pathway: TCR;EGFR1 (Consensus)

Recessive Scores

pRec: 0.167

Intolerance Scores

loftool: 0.367
rvis_EVS: -0.07
rvis_percentile_EVS: 48.78

Haploinsufficiency Scores

pHI: 0.159
hipred: Y
hipred_score: 0.825
ghis: 0.592

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.706

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ubash3b
Phenotype: immune system phenotype; normal phenotype; hematopoietic system phenotype;

Gene ontology

Biological process: negative regulation of protein kinase activity;negative regulation of signal transduction;peptidyl-tyrosine dephosphorylation;collagen-activated tyrosine kinase receptor signaling pathway;collagen-activated signaling pathway;regulation of protein binding;regulation of osteoclast differentiation;negative regulation of osteoclast differentiation;negative regulation of bone resorption;regulation of release of sequestered calcium ion into cytosol;platelet aggregation;negative regulation of platelet aggregation
Cellular component: nucleus;cytoplasm
Molecular function: protein tyrosine phosphatase activity;protein binding;phosphatase activity;ubiquitin protein ligase binding;identical protein binding;phosphoprotein binding