KDM5A p.Ser454=
c.1362T>A · rs183604048 · VCV735101
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.423%, eas)
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 -2.7, phastCons 1 |
| Overall | ||
| CADD | 10.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.423%
East Asian · 190/44,880 alleles
Filtering AF
0.374%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.355%
Overall
0.0122%
197/1,614,108 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.423% | 236 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,418 |
| European (non-Finnish) | 8.47e-05% | 1,179,949 |
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
- KDM5A
- Protein
- p.Ser454=
- Coding
- c.1362T>A
- MANE Select
- NM_001042603
- dbSNP
- rs183604048
- Type
- single nucleotide variant
- Location
- chr12:334369 (GRCh38)
- Gene constraint
- LOEUF 0.27 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 70.98 · 46 PDB
- Residue 454
- the jmjc domain
Similar variants
- KDM5A c.4074+1G>A Likely pathogenic ★★ same type
- KDM5A p.Ala1260Val Uncertain significance ★★ ⚠ same type
- KDM5A p.Ala736Thr Uncertain significance ★★ ⚠ same type
- KDM5A p.Glu1021Gly Uncertain significance ★★ ⚠ same type
- KDM5A p.Gly630Glu Uncertain significance ★★ ⚠ same type
- KDM5A p.Ile1011Thr Uncertain significance ★★ ⚠ same type
- KDM5A p.Ser479Cys Uncertain significance ★★ ⚠ same type
- KDM5A p.Ser572Cys Uncertain significance ★★ ⚠ 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/kdm5a-p-ser454 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown