KDM5C p.Ala388=
c.1164T>C · VCV4823353
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 2.6 | GERP -0.11, phastCons 1 |
| Overall | ||
| CADD | 11.37 | 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
- KDM5C
- Protein
- p.Ala388=
- Coding
- c.1164T>C
- MANE Select
- NM_004187
- Type
- single nucleotide variant
- Location
- chrX:53211865 (GRCh38)
- Structure
- AlphaFold pLDDT 72.50 · 2 PDB
- Residue 388
- a UniProt-annotated variant site (in mrxscj; impairs enzymatic activity and binding to h3-k9me3)
Similar variants
- KDM5C p.Ala388Pro Likely pathogenic ★ 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-ala388 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown