SH3BGR
protein-codingSH3 domain binding glutamate rich protein, the group of MicroRNA protein coding host genes
Gene summary
Predicted to enable protein-macromolecule adaptor activity. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~69.7 kbGenCC 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 SH3BGR variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_007341.3. 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 | 0 | |||||
| missense | 22 | 22 | ||||
| nonsense | 0 | |||||
| start loss | 1 | 1 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 24 | 0 | 0 | 24 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_031367.2 | 6 | MANE Select | |
| Ensembl | ENSP00000332513.5 | 6 | MANE Select | |
| RefSeq | NP_001001713.1 | 5 | Standard | |
| RefSeq | NP_001304669.2 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- positive regulation of signal transduction
- protein-containing complex assembly
Molecular Function
- SH3/SH2 adaptor activity
- SH3 domain binding
Cellular Component
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000333634
- Coding exons
- 6
- Length
- 69653
- Individuals with no LoFs
- 125685
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 61
- Defined
- 125747
- p
- 0.000247
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.442 | 114 | 128 | 0.890 | 0.00000643 | 1570 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00030 | 0.00030 | rare |
| South Asian | 0.00073 | 0.00065 | rare |
| Other | 0.00017 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0573
Intolerance Scores
- LoFtool
- 0.902
- RVIS EVS
- 1.3
- RVIS percentile EVS
- 93.95
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.143
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |