KDM5C p.Ala401=
c.1203C>T · rs782716338 · VCV744418
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0583%, sas)
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 -0.48 | GERP -4.5 |
| Overall | ||
| CADD | 4.843 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0583%
South Asian · 33/56,612 alleles
Filtering AF
0.0426%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0373%
Overall
0.00703%
85/1,209,147 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0583% | 1,716 |
| Remaining individualsnot grpmax-eligible | 0.00631% | 15,856 |
| European (non-Finnish) | 0.00525% | 19,031 |
| East Asian | 0.00296% | 33,758 |
| Admixed American | 0.00218% | 45,785 |
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.Ala401=
- Coding
- c.1203C>T
- MANE Select
- NM_004187
- dbSNP
- rs782716338
- Type
- single nucleotide variant
- Location
- chrX:53211826 (GRCh38)
- Structure
- AlphaFold pLDDT 72.50 · 2 PDB
- Residue 401
- an α-helix
Similar variants
- KDM5C p.Ala401Thr Uncertain significance ★ ⚠ same residue
- KDM5C c.1243-2A>G Pathogenic/Likely pathogenic ★★ same type
- KDM5C p.Arg332Ter Pathogenic ★★ same type
- KDM5C p.Arg599Cys Pathogenic/Likely pathogenic ★★ same type
- KDM5C p.Arg681Ter Pathogenic/Likely pathogenic ★★ same type
- KDM5C p.Arg68Ter Pathogenic ★★ same type
- KDM5C p.Arg750Trp Likely pathogenic ★★ same type
- KDM5C p.Arg778Ter 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/kdm5c-p-ala401 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown