KDM4B p.Ile758=
c.2274C>T · rs764335907 · VCV1335318
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0823%, mid)
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 -4.5 | GERP -3 |
| Overall | ||
| CADD | 1.711 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0823%
Middle Eastern · 5/6,078 alleles
Filtering AF
0.0323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.021%
Overall
0.00168%
27/1,607,600 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0823% | 1,216 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,138 |
| East Asian | 0.00224% | 44,646 |
| Admixed American | 0.00168% | 59,478 |
| European (non-Finnish) | 0.00136% | 73,634 |
| African / African-American | 0.00134% | 74,798 |
| South Asian | 0.00111% | 90,386 |
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.Ile758=
- Coding
- c.2274C>T
- MANE Select
- NM_015015
- dbSNP
- rs764335907
- Type
- single nucleotide variant
- Location
- chr19:5135527 (GRCh38)
- Gene constraint
- LOEUF 0.371 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 70.50 · 6 PDB
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-ile758 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown