AGK p.Glu130=
c.390G>A · rs771375243 · VCV987519
Likely pathogenic
No assertion criteria
Classification
Likely pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Sengers syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.86 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.78 | loss · gain 0.70 · SpliceAI calls gain · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | phastCons 1 |
| Overall | ||
| CADD | 28.6 | 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
- AGK
- Protein
- p.Glu130=
- Coding
- c.390G>A
- MANE Select
- NM_018238
- dbSNP
- rs771375243
- Type
- single nucleotide variant
- Location
- chr7:141611287 (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 130
- the dagkc domain
Disease context
Sengers syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Congenital cataract-hypertrophic cardiomyopathy-mitochondrial myopathy syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- AGK p.Glu130Ter Pathogenic ★ same residue
- AGK c.1047-2A>T Pathogenic/Likely pathogenic ★★ same condition
- AGK c.222-2A>C Likely pathogenic ★★ same condition
- AGK c.297+2T>C Pathogenic ★★ same condition
- AGK c.424-3C>G Pathogenic/Likely pathogenic ★★ same condition
- AGK c.518+1G>A Pathogenic ★★ same condition
- AGK p.Arg137Ter Pathogenic ★★ same condition
- AGK p.Arg138Ter 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-glu130 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown