KDM5C p.Ser643=
c.1929C>G · rs2146866093 · VCV3052750
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
KDM5C-related disorder
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 1.5 | GERP -3.2, phastCons 1 |
| Overall | ||
| CADD | 6.793 | 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.Ser643=
- Coding
- c.1929C>G
- MANE Select
- NM_004187
- dbSNP
- rs2146866093
- Type
- single nucleotide variant
- Location
- chrX:53201682 (GRCh38)
- Structure
- AlphaFold pLDDT 72.50 · 2 PDB
Disease context
KDM5C-related disorder
Similar variants
- KDM5C p.Arg929Ter Pathogenic/Likely pathogenic ★★ same condition
- KDM5C p.Arg943Ter Pathogenic/Likely pathogenic ★★ same condition
- KDM5C p.Pro554Thr Likely pathogenic ★★ same condition
- KDM5C p.Val504Met Pathogenic/Likely pathogenic ★★ same condition
- KDM5C p.Glu1521Asp Uncertain significance ★★ ⚠ same condition
- KDM5C p.Arg198Ter Pathogenic ★ same condition
- KDM5C p.Pro19Arg Likely pathogenic ★ same condition
- KDM5C p.Trp426Ter 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/kdm5c-p-ser643 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown