SH3BP4

SH3 domain binding protein 4

Basic information

Region (hg38): 2:234952016-235055714

Links

ENSG00000130147 ∙ NCBI:23677 ∙ OMIM:605611 ∙ HGNC:10826 ∙ Uniprot:Q9P0V3 ∙ 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 SH3BP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3BP4 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				5	6	11
missense			55	4	1	60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	9	7

Variants in SH3BP4

This is a list of pathogenic ClinVar variants found in the SH3BP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-235035008-G-A			Likely benign (Nov 01, 2022)
2-235035016-G-A		not specified	Uncertain significance (Mar 16, 2024)
2-235035022-G-A		not specified	Uncertain significance (Feb 28, 2023)
2-235035024-G-A		not specified	Uncertain significance (Feb 15, 2023)
2-235035025-C-T		not specified	Uncertain significance (Mar 25, 2024)
2-235035028-C-T			Uncertain significance (Nov 01, 2023)
2-235035031-A-G		not specified	Uncertain significance (Oct 22, 2021)
2-235035037-A-G		not specified	Likely benign (Oct 30, 2023)
2-235040890-C-T		not specified	Uncertain significance (Apr 09, 2024)
2-235040897-C-A		not specified	Uncertain significance (Jan 22, 2024)
2-235040919-C-A		not specified	Uncertain significance (Sep 17, 2021)
2-235040926-C-T		not specified	Uncertain significance (Oct 10, 2023)
2-235040931-C-T			Likely benign (Dec 01, 2023)
2-235040968-T-A		not specified	Uncertain significance (Nov 02, 2021)
2-235041113-G-A		not specified	Uncertain significance (Mar 29, 2024)
2-235041219-A-T		not specified	Uncertain significance (Jan 03, 2024)
2-235041224-C-T		not specified	Uncertain significance (Dec 08, 2023)
2-235041274-C-G		not specified	Uncertain significance (May 25, 2022)
2-235041274-C-T		not specified	Uncertain significance (Feb 28, 2024)
2-235041298-G-A		not specified	Uncertain significance (Mar 29, 2022)
2-235041301-A-T		not specified	Uncertain significance (May 25, 2022)
2-235041340-G-A		not specified	Uncertain significance (Jul 06, 2022)
2-235041364-A-C		not specified	Uncertain significance (Jan 31, 2024)
2-235041431-C-T		not specified	Uncertain significance (Oct 04, 2022)
2-235041433-G-A		not specified	Uncertain significance (Mar 26, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH3BP4	protein_coding	protein_coding	ENST00000409212	4	103742

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00253	0.997	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.628	539	582	0.927	0.0000380	6318
Missense in Polyphen		150	198.38	0.75611		2083
Synonymous	-0.644	281	268	1.05	0.0000201	1971
Loss of Function	3.35	10	29.7	0.337	0.00000153	325

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000438	0.000438
Ashkenazi Jewish	0.00169	0.00169
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000115	0.000114
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function in transferrin receptor internalization at the plasma membrane through a cargo-specific control of clathrin- mediated endocytosis. Alternatively, may act as a negative regulator of the amino acid-induced TOR signaling by inhibiting the formation of active Rag GTPase complexes. Preferentially binds inactive Rag GTPase complexes and prevents their interaction with the mTORC1 complex inhibiting its relocalization to lysosomes and its activation. Thereby, may indirectly regulate cell growth, proliferation and autophagy. {ECO:0000269|PubMed:16325581, ECO:0000269|PubMed:22575674}.
• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.472
• rvis_EVS: -0.72
• rvis_percentile_EVS: 14.28

Haploinsufficiency Scores

• pHI: 0.168
• hipred: Y
• hipred_score: 0.756
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.742

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh3bp4

Gene ontology

• Biological process: endocytosis;negative regulation of cell population proliferation;positive regulation of autophagy;negative regulation of cell growth;negative regulation of TOR signaling;negative regulation of GTPase activity;amino acid import;regulation of catalytic activity;protein localization to lysosome;cellular response to amino acid stimulus
• Cellular component: nucleus;cytoplasm;clathrin-coated pit;clathrin-coated vesicle;extracellular exosome
• Molecular function: GDP-dissociation inhibitor activity;protein binding;Ras GTPase binding;identical protein binding