AK2 p.Pro6=
c.18A>G · rs2522301993 · VCV2638616
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.54e-05%, 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 0.032 | GERP -3.1, phastCons 0.001 |
| Overall | ||
| CADD | 8.86 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.54e-05%
European (non-Finnish) · 1/1,171,410 alleles
Overall
6.27e-05%
1/1,594,542 alleles · very rare
exomes 1/1,442,220 · genomes 0/152,322 · joint denominator
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
- AK2
- Protein
- p.Pro6=
- Coding
- c.18A>G
- MANE Select
- NM_001625
- dbSNP
- rs2522301993
- Type
- single nucleotide variant
- Location
- chr1:33036811 (GRCh38)
- Gene constraint
- LOEUF 0.954 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.49 · 3 PDB
Similar variants
- AK2 c.330+5G>A Pathogenic ★★ same type
- AK2 c.498+1G>A Pathogenic/Likely pathogenic ★★ same type
- AK2 p.Ala182Asp Pathogenic/Likely pathogenic ★★ same type
- AK2 p.Arg103Trp Pathogenic/Likely pathogenic ★★ same type
- AK2 p.Arg175Pro Likely pathogenic ★★ same type
- AK2 p.Met1Val Pathogenic ★★ same type
- AK2 p.Ala212Thr Uncertain significance ★★ ⚠ same type
- AK2 p.Ala2Val 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/ak2-p-pro6 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown