UBASH3A

ubiquitin associated and SH3 domain containing A

Basic information

Region (hg38): 21:42403446-42447684

Links

ENSG00000160185 ∙ NCBI:53347 ∙ OMIM:605736 ∙ HGNC:12462 ∙ Uniprot:P57075 ∙ 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 UBASH3A gene.

• Inborn genetic diseases (32 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBASH3A 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	5	6
missense			29	3	1	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	29	4	6

Variants in UBASH3A

This is a list of pathogenic ClinVar variants found in the UBASH3A region.

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

Position	Type	Phenotype	Significance	ClinVar
21-42403967-C-A		not specified	Uncertain significance (Mar 29, 2022)
21-42403987-C-A		not specified	Uncertain significance (Dec 06, 2023)
21-42403995-A-G		not specified	Uncertain significance (Jul 29, 2022)
21-42404013-C-T		not specified	Likely benign (Aug 13, 2021)
21-42404015-C-T		not specified	Uncertain significance (Jan 31, 2024)
21-42404046-C-T		not specified	Uncertain significance (Mar 29, 2022)
21-42406340-C-T		not specified	Uncertain significance (Jan 04, 2022)
21-42406344-G-A			Likely benign (Jul 01, 2022)
21-42409538-G-T		not specified	Uncertain significance (Jul 29, 2022)
21-42409539-C-T		UBASH3A-related disorder	Likely benign (Jul 04, 2023)
21-42413032-C-A		not specified	Uncertain significance (Oct 06, 2021)
21-42413096-C-T		not specified	Uncertain significance (May 09, 2023)
21-42413101-G-T			Benign (Dec 11, 2017)
21-42413150-G-A		not specified	Likely benign (Jun 30, 2023)
21-42413177-C-T		not specified	Uncertain significance (Sep 20, 2023)
21-42413190-T-C		not specified	Uncertain significance (Sep 14, 2023)
21-42413198-G-A		not specified	Uncertain significance (Oct 29, 2021)
21-42413418-G-A		not specified	Uncertain significance (Dec 26, 2023)
21-42413505-C-T		not specified	Uncertain significance (May 09, 2022)
21-42416535-G-A		not specified	Uncertain significance (Jul 13, 2022)
21-42416564-T-C		not specified	Uncertain significance (Feb 13, 2024)
21-42416589-A-C		not specified	Uncertain significance (Jan 04, 2024)
21-42418437-G-A		not specified	Uncertain significance (Jun 21, 2023)
21-42418442-T-G		not specified	Uncertain significance (Aug 31, 2022)
21-42418472-C-T			Benign (Nov 03, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBASH3A	protein_coding	protein_coding	ENST00000319294	15	43784

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.05e-10	0.913	125679	0	69	125748	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.344	375	394	0.951	0.0000244	4300
Missense in Polyphen		118	137.01	0.86123		1496
Synonymous	0.0163	173	173	0.998	0.0000127	1282
Loss of Function	1.93	21	33.0	0.637	0.00000170	370

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000391	0.000389
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000347	0.000343
Middle Eastern	0.000218	0.000217
South Asian	0.000362	0.000359
Other	0.000326	0.000326

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, EGFR and PDGFRB, on the cell surface. Exhibits negligigle protein tyrosine phosphatase activity at neutral pH. May act as a dominant-negative regulator of UBASH3B-dependent dephosphorylation. May inhibit dynamin-dependent endocytic pathways by functionally sequestering dynamin via its SH3 domain. {ECO:0000269|PubMed:15159412, ECO:0000269|PubMed:17382318, ECO:0000269|PubMed:18189269}.

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.804
• rvis_EVS: -0.88
• rvis_percentile_EVS: 10.58

Haploinsufficiency Scores

• pHI: 0.159
• hipred: Y
• hipred_score: 0.541
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.543

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ubash3a
• Phenotype: vision/eye phenotype; immune system phenotype; normal phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: regulation of cytokine production;negative regulation of signal transduction;dephosphorylation;negative regulation of T cell receptor signaling pathway
• Cellular component: nucleoplasm;Golgi apparatus;cytosol;extracellular exosome
• Molecular function: protein binding;phosphatase activity