AGK p.Thr116=
c.348G>A · rs780162786 · VCV756126
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 -0.57 | |
| Overall | ||
| CADD | 8.965 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,078 alleles
Filtering AF
0.00177%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000892%
Overall
0.00062%
10/1,613,416 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,078 |
| East Asian | 0.00669% | 14,952 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,458 |
| African / African-American | 0.00134% | 74,906 |
| European (non-Finnish) | 0.000339% | 294,919 |
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.Thr116=
- Coding
- c.348G>A
- MANE Select
- NM_018238
- dbSNP
- rs780162786
- Type
- single nucleotide variant
- Location
- chr7:141611245 (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 116
- the dagkc domain
Similar variants
- AGK p.Thr116Met 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
- AGK p.Arg138Ter 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-thr116 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown