BCS1L p.Pro131=
c.393T>C · rs2106324185 · VCV1119534
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
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 -1 | GERP -5, phastCons 0.005 |
| Overall | ||
| CADD | 6.751 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,080 alleles
Overall
6.2e-05%
1/1,614,166 alleles · very rare
exomes 1/1,461,888 · genomes 0/152,278 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- BCS1L
- Protein
- p.Pro131=
- Coding
- c.393T>C
- MANE Select
- NM_001079866
- dbSNP
- rs2106324185
- Type
- single nucleotide variant
- Location
- chr2:218661478 (GRCh38)
- Gene constraint
- LOEUF 0.958 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.10
Similar variants
- BCS1L p.Pro131Leu Uncertain significance ★★ ⚠ same residue
- BCS1L p.Pro131Arg Uncertain significance ★ ⚠ same residue
- BCS1L c.320+1G>T Pathogenic/Likely pathogenic ★★ same type
- BCS1L c.321-2A>G Likely pathogenic ★★ same type
- BCS1L c.889+1G>T Pathogenic/Likely pathogenic ★★ same type
- BCS1L c.889+2T>G Likely pathogenic ★★ same type
- BCS1L c.-50+388C>G Likely pathogenic ★★ same type
- BCS1L c.-50+405A>G Pathogenic/Likely pathogenic ★★ 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/bcs1l-p-pro131 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown