AGK p.Asp323=
c.969C>T · rs775777094 · VCV3060197
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000863%, nfe)
Conditions
1
AGK-related disorder
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 0.59 | GERP 2.7, phastCons 0.89 |
| Overall | ||
| CADD | 5.88 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000863%
European (non-Finnish) · 10/1,159,358 alleles
Filtering AF
0.000436%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000318%
Overall
0.000703%
10/1,423,168 alleles · very rare
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.Asp323=
- Coding
- c.969C>T
- MANE Select
- NM_018238
- dbSNP
- rs775777094
- Type
- single nucleotide variant
- Location
- chr7:141641902 (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 323
- a UniProt-annotated variant site (in mtdps10)
Similar variants
- AGK c.222-2A>C Likely pathogenic ★★ same condition
- AGK c.297+2T>C Pathogenic ★★ same condition
- AGK p.Arg351Ter Likely pathogenic ★ same condition
- AGK p.Lys75Glu Uncertain significance ★ ⚠ same condition
- AGK c.-9C>G Likely benign same condition
- AGK p.Gln370= Likely benign same condition
- AGK p.Ile175fs Pathogenic/Likely pathogenic ★★ same condition
- AGK p.Arg210fs Likely pathogenic ★ same condition
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-asp323 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown