BEST1 p.Pro560=
c.1680A>T · rs2541417014 · VCV2098304
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 -0.52 | GERP -3.7 |
| Overall | ||
| CADD | 0.375 | 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
- BEST1
- Protein
- p.Pro560=
- Coding
- c.1680A>T
- MANE Select
- NM_004183
- dbSNP
- rs2541417014
- Type
- single nucleotide variant
- Location
- chr11:61962834 (GRCh38)
- Gene constraint
- LOEUF 1.28 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.46 · 19 PDB
Similar variants
- BEST1 p.Pro560Thr Uncertain significance ★ ⚠ same residue
- BEST1 c.1100+1G>C Pathogenic/Likely pathogenic ★★ same type
- BEST1 c.1101-1G>C Likely pathogenic ★★ same type
- BEST1 c.636+1G>A Pathogenic ★★ same type
- BEST1 c.867+97G>A Pathogenic/Likely pathogenic ★★ same type
- BEST1 p.Ala10Thr Pathogenic ★★ same type
- BEST1 p.Ala10Val Pathogenic ★★ same type
- BEST1 p.Ala195Val 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/best1-p-pro560 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown