KDM5C p.Ser287=
c.861G>A · rs61751238 · VCV589326
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0109%, amr)
Conditions
1
Inborn genetic diseases
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 -0.47 | GERP -3.3, phastCons 0.065 |
| Overall | ||
| CADD | 1.906 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0109%
Admixed American · 5/45,804 alleles
Filtering AF
0.00427%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00271%
Overall
0.00215%
26/1,209,420 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0109% | 9,161 |
| Remaining individualsnot grpmax-eligible | 0.0105% | 9,519 |
| European (non-Finnish) | 0.00179% | 55,912 |
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
- KDM5C
- Protein
- p.Ser287=
- Coding
- c.861G>A
- MANE Select
- NM_004187
- dbSNP
- rs61751238
- Type
- single nucleotide variant
- Location
- chrX:53215897 (GRCh38)
- Structure
- AlphaFold pLDDT 72.50 · 2 PDB
- Residue 287
- a modified residue (phosphoserine)
Similar variants
- KDM5C p.Ser287Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- KDM5C p.Arg68Ter Pathogenic ★★ same condition
- KDM5C p.Gln1020Ter Pathogenic ★★ same condition
- KDM5C p.Gln859Ter Pathogenic ★★ same condition
- KDM5C p.Glu698Lys Likely pathogenic ★★ same condition
- KDM5C p.Arg367Trp Uncertain significance ★★ ⚠ same condition
- KDM5C p.Arg909Trp Uncertain significance ★★ ⚠ same condition
- KDM5C p.Gln859Lys Uncertain significance ★★ ⚠ 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/kdm5c-p-ser287 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown