KDM5C p.Asp443=
c.1329C>T · rs782060947 · VCV1213368
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.014%, afr)
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 0.49 | GERP -3.9, phastCons 0.99 |
| Overall | ||
| CADD | 7.157 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.014%
African / African-American · 8/57,319 alleles
Filtering AF
0.00688%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00502%
Overall
0.000661%
8/1,209,723 alleles · ultra-rare
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.Asp443=
- Coding
- c.1329C>T
- MANE Select
- NM_004187
- dbSNP
- rs782060947
- Type
- single nucleotide variant
- Location
- chrX:53211569 (GRCh38)
- Structure
- AlphaFold pLDDT 72.50 · 2 PDB
- Residue 443
- a β-strand
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-asp443 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown