AK2 p.Leu73=
c.219G>C · rs587780848 · VCV136329
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.71 | donor loss at this position · masked 0 · deltas |
|---|---|---|
| Pangolin | Δ0.65 | loss · gain 0.06 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 5.9 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 20.1 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- AK2
- Protein
- p.Leu73=
- Coding
- c.219G>C
- MANE Select
- NM_001625
- dbSNP
- rs587780848
- Type
- single nucleotide variant
- Location
- chr1:33024442 (GRCh38)
- Gene constraint
- LOEUF 0.954 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.49 · 3 PDB
- Residue 73
- a binding site; a disulfide bond; the 'nmp' region; an α-helix
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-leu73 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown