KDM2B p.Ala660=
c.1980C>T · VCV3770891
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.108%, nfe)
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 -5.5 | GERP -4 |
| Overall | ||
| CADD | 11.85 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.108%
European (non-Finnish) · 1,272/1,174,420 alleles
Filtering AF
0.103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.101%
Overall
0.0836%
1,341/1,603,882 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.108% | 923 |
| Remaining individualsnot grpmax-eligible | 0.0515% | 1,941 |
| Middle Eastern | 0.0331% | 3,018 |
| African / African-American | 0.0214% | 4,675 |
| Admixed American | 0.017% | 5,881 |
| Finnishnot grpmax-eligible | 0.0079% | 12,665 |
| South Asian | 0.00335% | 29,884 |
| East Asian | 0.00225% | 44,516 |
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.Ala660=
- Coding
- c.1980C>T
- MANE Select
- NM_032590
- Type
- single nucleotide variant
- Location
- chr12:121445398 (GRCh38)
- Gene constraint
- LOEUF 0.266 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 68.20 · 4 PDB
Similar variants
- KDM2B p.Ala660Thr Uncertain significance ★ ⚠ same residue
- 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
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-ala660 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown