SH3BGRL3

SH3 domain binding glutamate rich protein like 3

Basic information

Region (hg38): 1:26280085-26281522

Links

ENSG00000142669 ∙ NCBI:83442 ∙ OMIM:615679 ∙ HGNC:15568 ∙ Uniprot:Q9H299 ∙ 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 SH3BGRL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3BGRL3 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in SH3BGRL3

This is a list of pathogenic ClinVar variants found in the SH3BGRL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-26280160-G-A		not specified	Uncertain significance (Nov 30, 2021)
1-26280162-G-T		not specified	Uncertain significance (Sep 07, 2022)
1-26280793-G-A		not specified	Uncertain significance (Dec 21, 2023)
1-26280866-G-T		not specified	Uncertain significance (Mar 25, 2024)
1-26280871-C-T		not specified	Uncertain significance (Aug 12, 2021)
1-26280919-A-G		not specified	Uncertain significance (Mar 21, 2023)
1-26281073-G-C		not specified	Uncertain significance (Mar 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH3BGRL3	protein_coding	protein_coding	ENST00000270792	3	2341

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.149	0.784	125723	0	11	125734	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.266	47	52.4	0.897	0.00000289	591
Missense in Polyphen		4	13.976	0.2862		202
Synonymous	0.389	22	24.4	0.900	0.00000147	183
Loss of Function	1.50	2	5.93	0.337	4.23e-7	52

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000277	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could act as a modulator of glutaredoxin biological activity.
• Pathway: miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase (Consensus)

Recessive Scores

• pRec: 0.0885

Intolerance Scores

• loftool: 0.660
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• pHI: 0.127
• hipred: N
• hipred_score: 0.444
• ghis: 0.628

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.165

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh3bgrl3
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: electron transport chain;cell redox homeostasis
• Cellular component: cytoplasm;nuclear body;extracellular exosome
• Molecular function: electron transfer activity;protein disulfide oxidoreductase activity