BCAR1 p.Phe339=
c.1017T>C · rs2507383211 · VCV3027276
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.19 | GERP -3.3, phastCons 0.013 |
| Overall | ||
| CADD | 3.236 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- BCAR1
- Protein
- p.Phe339=
- Coding
- c.1017T>C
- MANE Select
- NM_014567
- dbSNP
- rs2507383211
- Type
- single nucleotide variant
- Location
- chr16:75235882 (GRCh38)
- Gene constraint
- LOEUF 0.778 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.07 · 5 PDB
- Residue 339
- the 'substrate for kinases' region
Similar variants
- BCAR1 c.2100+10C>T Benign/Likely benign ★★ same type
- BCAR1 p.Ala411= Benign ★★ same type
- BCAR1 p.Ala514= Benign ★★ same type
- BCAR1 p.Ala590Thr Benign ★★ ⚠ same type
- BCAR1 p.Arg491Leu Benign ★★ same type
- BCAR1 p.Gly450Val Benign ★★ same type
- BCAR1 p.Gly568Ser Benign ★★ same type
- BCAR1 p.His558Arg Benign ★★ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/bcar1-p-phe339 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown