AK1 p.Ser49=
c.147A>G · VCV3627823
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00669%, eas)
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 -10 | GERP -4.9 |
| Overall | ||
| CADD | 0.745 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00669%
East Asian · 3/44,872 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000891%
Overall
0.000248%
4/1,613,912 alleles · very rare
exomes 4/1,461,626 · genomes 0/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00669% | 14,957 |
| European (non-Finnish) | 8.48e-05% | 1,179,791 |
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
- AK1
- Protein
- p.Ser49=
- Coding
- c.147A>G
- MANE Select
- NM_000476
- Type
- single nucleotide variant
- Location
- chr9:127872750 (GRCh38)
- Gene constraint
- LOEUF 0.873 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 95.82 · 5 PDB
- Residue 49
- the 'nmp' region
Similar variants
- AK1 p.Arg107Ter Pathogenic/Likely pathogenic ★★ same type
- AK1 p.Arg77Gln Uncertain significance ★★ ⚠ same type
- AK1 p.Arg77Trp Uncertain significance ★★ same type
- AK1 p.Glu26Asp Uncertain significance ★★ ⚠ same type
- AK1 p.Gly137Arg Uncertain significance ★★ ⚠ same type
- AK1 p.Gly177Asp Uncertain significance ★★ ⚠ same type
- AK1 p.Ile169Thr Uncertain significance ★★ same type
- AK1 p.Met80Val 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/ak1-p-ser49 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown