KDM5C p.Glu76=
c.228G>A · rs2519599152 · VCV2801446
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Spastic paraplegia
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.39 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.21 | loss · gain 0.04 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 4.9 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 21.3 | 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.Glu76=
- Coding
- c.228G>A
- MANE Select
- NM_004187
- dbSNP
- rs2519599152
- Type
- single nucleotide variant
- Location
- chrX:53220839 (GRCh38)
- Structure
- AlphaFold pLDDT 72.50 · 2 PDB
- Residue 76
- an α-helix
Similar variants
- KDM5C p.Glu76Gln Uncertain significance ★ ⚠ same residue
- KDM5C c.1243-2A>G Pathogenic/Likely pathogenic ★★ same condition
- KDM5C p.Arg681Ter Pathogenic/Likely pathogenic ★★ same condition
- KDM5C p.Arg750Trp Likely pathogenic ★★ same condition
- KDM5C p.Arg778Ter Pathogenic ★★ same condition
- KDM5C p.Gln588Ter Pathogenic ★★ same condition
- KDM5C c.4038+6C>G Uncertain significance ★★ same condition
- KDM5C p.Ala1085Ser 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-glu76 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown