KDM1A p.Pro87=
c.261T>C · rs767187910 · VCV2038736
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00754%, nfe)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.83 | GERP -2.5, phastCons 0.95 |
| Overall | ||
| CADD | 13.28 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00754%
European (non-Finnish) · 86/1,140,002 alleles
Filtering AF
0.00625%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00576%
Overall
0.00564%
86/1,525,228 alleles · very rare
exomes 85/1,373,128 · genomes 1/152,100 · joint denominator
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
- KDM1A
- Protein
- p.Pro87=
- Coding
- c.261T>C
- MANE Select
- NM_001009999
- dbSNP
- rs767187910
- Type
- single nucleotide variant
- Location
- chr1:23019857 (GRCh38)
- Gene constraint
- LOEUF 0.638 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.29 · 129 PDB
- Residue 87
- the 'disordered' region
Similar variants
- KDM1A p.Pro87Ala Uncertain significance ★★ ⚠ same residue
- KDM1A p.Ala10Val Uncertain significance ★★ ⚠ same condition
- KDM1A p.Ala11Ser Uncertain significance ★★ ⚠ same condition
- KDM1A p.Ala11Thr Uncertain significance ★★ ⚠ same condition
- KDM1A p.Ala12Val Uncertain significance ★★ ⚠ same condition
- KDM1A p.Ala13Thr Uncertain significance ★★ ⚠ same condition
- KDM1A p.Ala18Thr Uncertain significance ★★ ⚠ same condition
- KDM1A p.Ala197Thr 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/kdm1a-p-pro87 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown