SH3BGRL2

SH3 domain binding glutamate rich protein like 2

Basic information

Region (hg38): 6:79537185-79703655

Links

ENSG00000198478 ∙ NCBI:83699 ∙ OMIM:615678 ∙ HGNC:15567 ∙ Uniprot:Q9UJC5 ∙ 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 SH3BGRL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SH3BGRL2 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			3	1		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	1	0

Variants in SH3BGRL2

This is a list of pathogenic ClinVar variants found in the SH3BGRL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-79537224-C-T		Leber congenital amaurosis	Uncertain significance (Jun 14, 2016)
6-79537237-T-G		Leber congenital amaurosis 5	Uncertain significance (Jan 13, 2018)
6-79537277-T-A		Leber congenital amaurosis 5	Uncertain significance (Jan 12, 2018)
6-79537307-G-A		Leber congenital amaurosis 5	Benign (Apr 28, 2017)
6-79537321-G-A		Leber congenital amaurosis 5	Uncertain significance (Jan 12, 2018)
6-79537371-C-A		Leber congenital amaurosis 5	Uncertain significance (Jan 13, 2018)
6-79537371-C-G		Leber congenital amaurosis 5	Conflicting classifications of pathogenicity (Nov 01, 2022)
6-79537373-C-A		Leber congenital amaurosis 5	Uncertain significance (Jan 13, 2018)
6-79537387-G-A		Leber congenital amaurosis 5	Uncertain significance (Jan 12, 2018)
6-79537397-G-C		Leber congenital amaurosis 5	Uncertain significance (Jan 13, 2018)
6-79537402-C-T		Leber congenital amaurosis 5	Uncertain significance (Jan 13, 2018)
6-79673725-G-A		not specified	Likely benign (Oct 27, 2022)
6-79696507-C-A		not specified	Uncertain significance (Oct 02, 2023)
6-79696549-C-T		not specified	Uncertain significance (Jan 19, 2024)
6-79696551-C-T		not specified	Uncertain significance (Sep 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SH3BGRL2	protein_coding	protein_coding	ENST00000369838	4	72373

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.60e-7	0.0692	125719	0	16	125735	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00750	57	57.2	0.997	0.00000296	697
Missense in Polyphen		25	24.317	1.0281		323
Synonymous	0.478	19	21.8	0.870	0.00000122	185
Loss of Function	-0.895	9	6.53	1.38	3.62e-7	73

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000153	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000629	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.649
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.11

Haploinsufficiency Scores

• pHI: 0.169
• hipred: N
• hipred_score: 0.352
• ghis: 0.541

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sh3bgrl2

Gene ontology

• Cellular component: nucleoplasm;nuclear membrane
• Molecular function: SH3 domain binding