KDM2B p.Pro535=
c.1605C>T · rs375353232 · VCV714574
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
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 -8.1 | GERP -3.9 |
| Overall | ||
| CADD | 1.57 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,806 alleles
Filtering AF
0.000444%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000744%
12/1,613,574 alleles · very rare
exomes 10/1,461,708 · genomes 2/151,866 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,403 |
| East Asian | 0.00223% | 44,850 |
| South Asian | 0.0022% | 45,537 |
| European (non-Finnish) | 0.000593% | 168,570 |
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
- KDM2B
- Protein
- p.Pro535=
- Coding
- c.1605C>T
- MANE Select
- NM_032590
- dbSNP
- rs375353232
- Type
- single nucleotide variant
- Location
- chr12:121509609 (GRCh38)
- Gene constraint
- LOEUF 0.266 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 68.20 · 4 PDB
Similar variants
- KDM2B p.Arg614Pro Pathogenic/Likely pathogenic ★★ same type
- KDM2B p.Cys616Arg Pathogenic/Likely pathogenic ★★ same type
- KDM2B p.Gly638Asp Pathogenic ★★ same type
- KDM2B p.Arg1124Gln Uncertain significance ★★ ⚠ same type
- KDM2B p.Arg294Gln Uncertain significance ★★ ⚠ same type
- KDM2B p.Arg612Gln Uncertain significance ★★ ⚠ same type
- KDM2B p.Asn742Lys Uncertain significance ★★ ⚠ same type
- KDM2B p.Glu922Lys 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/kdm2b-p-pro535 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown