ALKBH2 p.Pro217=
c.651G>A · VCV3856410
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00668%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.014 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 9.922 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00668%
East Asian · 3/44,886 alleles
Filtering AF
0.00255%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00162%
Overall
0.000991%
16/1,613,918 alleles · very rare
exomes 12/1,461,862 · genomes 4/152,056 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00668% | 14,962 |
| African / African-American | 0.00668% | 14,978 |
| Admixed American | 0.005% | 19,991 |
| European (non-Finnish) | 0.000424% | 236,000 |
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
- ALKBH2
- Protein
- p.Pro217=
- Coding
- c.651G>A
- MANE Select
- NM_001145374
- Type
- single nucleotide variant
- Location
- chr12:109088341 (GRCh38)
- Gene constraint
- LOEUF 1.392 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.23 · 18 PDB
- Residue 217
- the fe2og dioxygenase domain; a β-strand
Similar variants
- ALKBH2 p.Ala118Gly Uncertain significance ★ ⚠ same type
- ALKBH2 p.Ala246Val Uncertain significance ★ ⚠ same type
- ALKBH2 p.Ala78Thr Uncertain significance ★ ⚠ same type
- ALKBH2 p.Arg142Trp Uncertain significance ★ ⚠ same type
- ALKBH2 p.Arg176Lys Uncertain significance ★ ⚠ same type
- ALKBH2 p.Arg198Gln Uncertain significance ★ ⚠ same type
- ALKBH2 p.Arg248Trp Uncertain significance ★ ⚠ same type
- ALKBH2 p.Arg254Cys 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/alkbh2-p-pro217 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown