AGK p.Pro86=
c.258G>A · rs773960062 · VCV2658094
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00893%, 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 -2.7 | GERP -8.6 |
| Overall | ||
| CADD | 6.865 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00893%
East Asian · 4/44,794 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0018%
Overall
0.00062%
10/1,612,668 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00893% | 11,198 |
| South Asian | 0.0011% | 90,956 |
| European (non-Finnish) | 0.000424% | 235,877 |
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
- AGK
- Protein
- p.Pro86=
- Coding
- c.258G>A
- MANE Select
- NM_018238
- dbSNP
- rs773960062
- Type
- single nucleotide variant
- Location
- chr7:141601241 (GRCh38)
- Gene constraint
- LOEUF 0.918 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.93 · 2 PDB
- Residue 86
- the dagkc domain
Similar variants
- AGK p.Pro86Leu Uncertain significance ★★ ⚠ same residue
- AGK p.Pro86Arg Uncertain significance ★ ⚠ same residue
- AGK c.1047-2A>T Pathogenic/Likely pathogenic ★★ same type
- AGK c.222-2A>C Likely pathogenic ★★ same type
- AGK c.297+2T>C Pathogenic ★★ same type
- AGK c.424-3C>G Pathogenic/Likely pathogenic ★★ same type
- AGK c.518+1G>A Pathogenic ★★ same type
- AGK p.Arg137Ter Pathogenic ★★ 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/agk-p-pro86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown