SH3BGR

SH3 domain binding glutamate rich protein, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 21:39445854-39515506

Links

ENSG00000185437 ∙ NCBI:6450 ∙ OMIM:602230 ∙ HGNC:10822 ∙ Uniprot:P55822 ∙ 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 SH3BGR gene.

• Inborn genetic diseases (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3BGR 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	12	0	0

Variants in SH3BGR

This is a list of pathogenic ClinVar variants found in the SH3BGR region.

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

Position	Type	Phenotype	Significance	ClinVar
21-39451954-G-A		not specified	Uncertain significance (Feb 06, 2023)
21-39451962-C-T		not specified	Uncertain significance (Dec 05, 2022)
21-39451977-C-T		not specified	Uncertain significance (Jan 17, 2024)
21-39452001-C-G		not specified	Uncertain significance (Jul 19, 2022)
21-39452088-A-C		not specified	Uncertain significance (Jan 10, 2023)
21-39452098-T-C		not specified	Uncertain significance (Dec 12, 2023)
21-39452140-C-T		not specified	Uncertain significance (Mar 20, 2023)
21-39462392-A-T		not specified	Uncertain significance (Sep 27, 2021)
21-39462396-G-A		not specified	Uncertain significance (Sep 01, 2021)
21-39462415-C-T		not specified	Uncertain significance (Nov 21, 2023)
21-39462459-G-A		not specified	Uncertain significance (Jun 29, 2023)
21-39475204-C-G		not specified	Uncertain significance (Nov 03, 2022)
21-39499830-A-G		not specified	Uncertain significance (Jul 05, 2023)
21-39499845-G-A		not specified	Uncertain significance (Nov 08, 2022)
21-39499871-G-A		not specified	Uncertain significance (Feb 23, 2023)
21-39511695-A-G		not specified	Uncertain significance (Aug 11, 2022)
21-39511714-A-C		not specified	Uncertain significance (Aug 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH3BGR	protein_coding	protein_coding	ENST00000333634	6	69653

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00218	0.926	125685	1	61	125747	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.442	114	128	0.890	0.00000643	1570
Missense in Polyphen		22	25.295	0.86973		353
Synonymous	0.0475	46	46.4	0.991	0.00000263	440
Loss of Function	1.57	6	11.8	0.507	5.01e-7	160

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000248	0.000247
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000555	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000303	0.000299
Middle Eastern	0.0000555	0.0000544
South Asian	0.000735	0.000653
Other	0.000168	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0573

Intolerance Scores

• loftool: 0.902
• rvis_EVS: 1.3
• rvis_percentile_EVS: 93.95

Haploinsufficiency Scores

• pHI: 0.0549
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.143

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh3bgr

Gene ontology

• Biological process: positive regulation of signal transduction;protein-containing complex assembly
• Cellular component: cytosol
• Molecular function: SH3/SH2 adaptor activity;SH3 domain binding