KDM6B p.Pro646=
c.1938A>C · rs1481951407 · VCV2647403
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00226%, 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 0.73 | GERP -2.9, phastCons 0.98 |
| Overall | ||
| CADD | 6.057 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00226%
East Asian · 1/44,322 alleles
Overall
0.000686%
1/145,784 alleles · very 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
- KDM6B
- Protein
- p.Pro646=
- Coding
- c.1938A>C
- MANE Select
- NM_001348716
- dbSNP
- rs1481951407
- Type
- single nucleotide variant
- Location
- chr17:7848226 (GRCh38)
- Gene constraint
- LOEUF 0.211 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 58.54 · 6 PDB
- Residue 646
- 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-pro646 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown