SH3BP5

SH3 domain binding protein 5

Basic information

Region (hg38): 3:15254352-15341368

Links

ENSG00000131370 ∙ NCBI:9467 ∙ OMIM:605612 ∙ HGNC:10827 ∙ Uniprot:O60239 ∙ 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 SH3BP5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3BP5 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						0
missense			22			22
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region					1	1
non coding			3			3
Total	0	0	26	1	0

Variants in SH3BP5

This is a list of pathogenic ClinVar variants found in the SH3BP5 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-15256129-C-T		not specified	Uncertain significance (Feb 23, 2023)
3-15256165-C-T		not specified	Uncertain significance (May 29, 2024)
3-15256174-A-C		not specified	Uncertain significance (Nov 09, 2021)
3-15256246-C-G		not specified	Uncertain significance (Mar 06, 2023)
3-15256253-T-G		not specified	Uncertain significance (Dec 26, 2023)
3-15256273-G-C		not specified	Uncertain significance (Dec 22, 2023)
3-15256289-CTTCTGCCCTGTCTCCTATAGAAATACAAGGATTATCAAAAGTGAGTATTGACAA-C			Likely benign (Aug 08, 2018)
3-15256306-A-G			Benign (Mar 29, 2018)
3-15257029-C-T		not specified	Uncertain significance (Aug 16, 2021)
3-15257047-T-C		not specified	Uncertain significance (Nov 27, 2023)
3-15257070-CA-C			Uncertain significance (Feb 01, 2024)
3-15257081-T-C		not specified	Uncertain significance (Jan 31, 2024)
3-15258938-C-T		not specified	Uncertain significance (Jun 17, 2024)
3-15258965-A-G		not specified	Uncertain significance (May 14, 2024)
3-15259025-A-C		not specified	Uncertain significance (Apr 13, 2022)
3-15259032-C-T		not specified	Uncertain significance (Oct 06, 2021)
3-15259039-C-G		not specified	Uncertain significance (Jun 04, 2024)
3-15259786-T-G		not specified	Uncertain significance (May 18, 2022)
3-15262167-G-C		not specified	Uncertain significance (Jan 19, 2024)
3-15262196-G-C		not specified	Uncertain significance (Apr 20, 2023)
3-15262207-C-T		not specified	Uncertain significance (Mar 20, 2023)
3-15262222-T-C		not specified	Uncertain significance (Dec 05, 2022)
3-15262249-A-G		not specified	Uncertain significance (Dec 12, 2023)
3-15269736-T-G		not specified	Uncertain significance (Jan 08, 2024)
3-15269762-C-T		not specified	Uncertain significance (Apr 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH3BP5	protein_coding	protein_coding	ENST00000383791	9	86516

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0483	0.951	125735	0	12	125747	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.962	226	271	0.835	0.0000157	2976
Missense in Polyphen		45	76.51	0.58816		828
Synonymous	-1.40	127	108	1.17	0.00000653	875
Loss of Function	2.91	6	20.0	0.299	0.00000103	239

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000443	0.0000439
Middle Eastern	0.000163	0.000163
South Asian	0.0000983	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Inhibits the auto- and transphosphorylation activity of BTK. Plays a negative regulatory role in BTK-related cytoplasmic signaling in B-cells. May be involved in BCR-induced apoptotic cell death. {ECO:0000269|PubMed:10339589, ECO:0000269|PubMed:9571151}.
• Pathway: BCR signaling pathway (Consensus)

Recessive Scores

• pRec: 0.271

Intolerance Scores

• loftool: 0.120
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.6

Haploinsufficiency Scores

• pHI: 0.339
• hipred: Y
• hipred_score: 0.763
• ghis: 0.413

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.796

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh3bp5
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: signal transduction;intracellular signal transduction;negative regulation of protein tyrosine kinase activity
• Cellular component: nucleoplasm;cytoplasm;mitochondrion;nuclear body
• Molecular function: protein kinase inhibitor activity;protein binding;SH3 domain binding