UBASH3B

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

Basic information

Region (hg38): 11:122655721-122814473

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.

• Inborn genetic diseases (22 variants)
• not provided (9 variants)

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.

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	3	6
missense			22	1	1	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	22	4	5

Variants in UBASH3B

This is a list of pathogenic ClinVar variants found in the UBASH3B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-122656107-A-G		not specified	Uncertain significance (Oct 12, 2022)
11-122656113-G-C			Likely benign (Jul 01, 2022)
11-122656123-G-C		not specified	Uncertain significance (Jun 11, 2021)
11-122776228-C-G			Benign (May 04, 2018)
11-122776240-G-A			Likely benign (Jun 27, 2018)
11-122776251-G-A		not specified	Uncertain significance (Mar 29, 2023)
11-122777079-G-A		not specified	Uncertain significance (Aug 05, 2023)
11-122777123-C-T			Benign (Jun 29, 2018)
11-122777124-G-A		not specified	Uncertain significance (Mar 11, 2022)
11-122779487-T-C			Benign (Jun 29, 2018)
11-122779650-A-C		not specified	Uncertain significance (Dec 21, 2022)
11-122779675-C-T		not specified	Uncertain significance (Jun 07, 2023)
11-122783178-G-C		not specified	Uncertain significance (Sep 16, 2021)
11-122789125-C-T		not specified	Uncertain significance (Apr 11, 2023)
11-122789160-G-A		not specified	Uncertain significance (Jul 14, 2022)
11-122789180-T-G			Likely benign (Jul 01, 2022)
11-122789181-C-T		not specified	Uncertain significance (Aug 02, 2022)
11-122789238-G-A		not specified	Uncertain significance (Jan 03, 2024)
11-122794722-C-T		not specified	Uncertain significance (Apr 26, 2023)
11-122794728-C-T		not specified	Uncertain significance (Jan 04, 2024)
11-122794761-T-C		not specified	Uncertain significance (Mar 06, 2023)
11-122794820-T-A		not specified	Uncertain significance (Apr 25, 2022)
11-122796180-G-A			Benign (Mar 29, 2018)
11-122796191-G-A			Likely benign (May 24, 2018)
11-122796911-G-T		not specified	Uncertain significance (May 30, 2023)

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