KDM5C p.Phe697=
c.2091C>T · rs782198070 · VCV771598
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0939%, 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 -0.023 | GERP -5.7, phastCons 0.012 |
| Overall | ||
| CADD | 1.158 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0939%
Admixed American · 43/45,799 alleles
Filtering AF
0.0716%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0637%
Overall
0.00454%
55/1,210,219 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0939% | 1,065 |
| South Asian | 0.00352% | 28,436 |
| European (non-Finnish) | 0.00112% | 89,523 |
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.Phe697=
- Coding
- c.2091C>T
- MANE Select
- NM_004187
- dbSNP
- rs782198070
- Type
- single nucleotide variant
- Location
- chrX:53199129 (GRCh38)
- Structure
- AlphaFold pLDDT 72.50 · 2 PDB
- Residue 697
- an α-helix
Similar variants
- 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
- KDM5C p.Glu1276Lys 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-phe697 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown