SH3BGRL

protein-coding

SH3 domain binding glutamate rich protein like

Gene summary

Enables protein-RNA adaptor activity and ubiquitin-like ligase-substrate adaptor activity. Involved in positive regulation of cytoplasmic translational initiation and proteasome-mediated ubiquitin-dependent protein catabolic process. Located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_003022.3

Inheritance

—

ClinVar variants

U:35

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chrX:81,202,102-81,298,547

External References & Databases

Ensembl (ENSG00000131171)

Transcript & Mutation Effects

hg38 • Region Span ~96.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SH3BGRL variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003022.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar			5
missense			17 clinvar			17
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			11 clinvar			11
Total	0	0	35	0	0	35

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003022.3	RefSeq	NP_003013.1	4	MANE Select
ENST00000373212.6	Ensembl	ENSP00000362308.5	4	MANE Select
ENST00000877843.1	Ensembl	ENSP00000547902.1	3	Standard
ENST00000877843.2	Ensembl	ENSP00000547902.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

EGFR1

Biological Process

positive regulation of signal transduction

Molecular Function

SH3/SH2 adaptor activity
SH3 domain binding

Cellular Component

extracellular space
nucleus
cytoplasm
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373212
Coding exons: 4
Length: 96605
Individuals with no LoFs: 108059
Homozygous LoFs: 1
Heterozygous LoFs: 0
Defined: 108060
p: 0.00000463

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.528	29	38.2	0.759	0.00000278	745
Missense (PolyPhen)		9	13.262	0.67864		286
Synonymous	-1.13	18	12.8	1.40	8.86e-7	210
Loss of Function	1.39	1	3.99	0.251	3.03e-7	74

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0.000067	0.000044	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.142

Intolerance Scores

LoFtool: 0.362
RVIS EVS: 0.01
RVIS percentile EVS: 54.63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.801

Gene Damage Prediction

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