BEAN1 p.Pro214Ser
c.640C>T · VCV3337851
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
ambiguous
0.5396 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
1/2 damaging
REVEL, SaProt · AlphaMissense indeterminate
Computational evidence
| Protein change | ||
| AlphaMissense | 0.5396 | ambiguous |
|---|---|---|
| REVEL | 0.205 | benign-leaning |
| SaProt | LLR -13.97 | damaging |
| ⇒ SaProt calls this damaging; REVEL does not; AlphaMissense is indeterminate. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 5.4 | GERP 0.7, phastCons 1 |
| Regional constraint | o/e 0.96 | unconstrained · MANE · 43 kb · p 0.44 · regional, not allelic |
| Overall | ||
| CADD | 24.5 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
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
- BEAN1
- Protein
- p.Pro214Ser
- Coding
- c.640C>T
- MANE Select
- NM_001178020
- Type
- single nucleotide variant
- Location
- chr16:66480785 (GRCh38)
- Gene constraint
- LOEUF 1.45 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.44
- Residue 214
- the 'disordered' region
Similar variants
- BEAN1 p.Ala156Ser Uncertain significance ★★ ⚠ same type
- BEAN1 p.Arg90Gln Uncertain significance ★★ ⚠ same type
- BEAN1 p.Arg108His Likely benign ★★ same type
- BEAN1 p.Arg76Ser Benign/Likely benign ★★ same type
- BEAN1 p.Pro167= Likely benign ★★ same type
- BEAN1 p.Tyr216= Likely benign ★★ same type
- BEAN1 p.Tyr96= Likely benign ★★ same type
- BEAN1 p.Ala10Thr Uncertain significance ★ ⚠ 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/bean1-p-pro214ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown