KDM6B p.Pro625=
c.1875G>A · rs201687384 · VCV2647402
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0491%, 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 8.1 | GERP 0.35, phastCons 1 |
| Overall | ||
| CADD | 13.58 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0491%
East Asian · 22/44,828 alleles
Filtering AF
0.035%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0311%
Overall
0.0044%
71/1,612,608 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0491% | 2,038 |
| South Asian | 0.0461% | 2,168 |
| European (non-Finnish) | 0.000593% | 168,556 |
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
- KDM6B
- Protein
- p.Pro625=
- Coding
- c.1875G>A
- MANE Select
- NM_001348716
- dbSNP
- rs201687384
- Type
- single nucleotide variant
- Location
- chr17:7848163 (GRCh38)
- Gene constraint
- LOEUF 0.211 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.54 · 6 PDB
- Residue 625
- the 'disordered' region; a UniProt-annotated variant site (in nedsst)
Similar variants
- KDM6B p.Arg1499Ter Pathogenic/Likely pathogenic ★★ same type
- KDM6B p.Arg166Ter Pathogenic ★★ same type
- KDM6B p.Arg199Ter Pathogenic/Likely pathogenic ★★ same type
- KDM6B p.Arg229Ter Pathogenic/Likely pathogenic ★★ same type
- KDM6B p.Arg495Ter Pathogenic/Likely pathogenic ★★ same type
- KDM6B p.Arg951Ter Pathogenic ★★ same type
- KDM6B p.Ala1219Val Uncertain significance ★★ ⚠ same type
- KDM6B p.Ala750Thr 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/kdm6b-p-pro625 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown