KDM4B p.Pro353=
c.1059C>T · rs139508576 · VCV782320
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.125%, 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 -12 | GERP -3.4 |
| Overall | ||
| CADD | 0.785 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.125%
East Asian · 56/44,718 alleles
Filtering AF
0.099%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0895%
Overall
0.0168%
270/1,609,400 alleles · rare
exomes 246/1,457,158 · genomes 24/152,242 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.125% | 799 |
| Remaining individualsnot grpmax-eligible | 0.0161% | 6,229 |
| European (non-Finnish) | 0.016% | 6,235 |
| African / African-American | 0.0147% | 6,808 |
| South Asian | 0.00442% | 22,645 |
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
- KDM4B
- Protein
- p.Pro353=
- Coding
- c.1059C>T
- MANE Select
- NM_015015
- dbSNP
- rs139508576
- Type
- single nucleotide variant
- Location
- chr19:5110762 (GRCh38)
- Gene constraint
- LOEUF 0.371 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 70.50 · 6 PDB
- Residue 353
- an α-helix
Similar variants
- KDM4B c.432+1G>A Pathogenic/Likely pathogenic ★★ same type
- KDM4B p.His768Arg Likely pathogenic ★★ same type
- KDM4B p.Ala187Thr Uncertain significance ★★ ⚠ same type
- KDM4B p.Ala651Asp Uncertain significance ★★ ⚠ same type
- KDM4B p.Ala706Gly Uncertain significance ★★ ⚠ same type
- KDM4B p.Ala759Thr Uncertain significance ★★ ⚠ same type
- KDM4B p.Arg1020His Uncertain significance ★★ ⚠ same type
- KDM4B p.Arg1035Cys 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/kdm4b-p-pro353 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown