RAD50 p.Ser287=
c.861T>C · rs1042907420 · VCV414959
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00127%, nfe)
Conditions
1
hereditary neoplastic syndrome
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 1.9 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 9.302 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00127%
European (non-Finnish) · 15/1,179,864 alleles
Filtering AF
0.000763%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000605%
Overall
0.00093%
15/1,613,636 alleles · very rare
exomes 13/1,461,460 · genomes 2/152,176 · 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
- RAD50
- Protein
- p.Ser287=
- Coding
- c.861T>C
- MANE Select
- NM_005732
- dbSNP
- rs1042907420
- Type
- single nucleotide variant
- Location
- chr5:132587666 (GRCh38)
- Gene constraint
- LOEUF 0.889 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 82.83 · 6 PDB
Similar variants
- RAD50 p.Ser287Arg Uncertain significance ★★ ⚠ same residue
- RAD50 p.Ser287Asn Uncertain significance ★★ ⚠ same residue
- RAD50 p.Ser287Gly Uncertain significance ★ ⚠ same residue
- RAD50 c.1051+1G>A Likely pathogenic ★★ same condition
- RAD50 c.1052-1G>A Likely pathogenic ★★ same condition
- RAD50 c.1052-1G>T Pathogenic/Likely pathogenic ★★ same condition
- RAD50 c.1052-2A>C Likely pathogenic ★★ same condition
- RAD50 c.1245+1G>A Pathogenic/Likely pathogenic ★★ same condition
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/rad50-p-ser287 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown