AGK p.Arg9=
c.25C>A · rs139967538 · VCV2430905
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.41 | acceptor loss, 38 bp away · masked 0 · deltas |
|---|---|---|
| Pangolin | Δ0.34 | loss · gain 0.03 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 3.3 | GERP 3.4, phastCons 1 |
| Overall | ||
| CADD | 5.884 | 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.Arg9=
- Coding
- c.25C>A
- MANE Select
- NM_018238
- dbSNP
- rs139967538
- Type
- single nucleotide variant
- Location
- chr7:141555491 (GRCh38)
- Gene constraint
- LOEUF 0.918 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.93 · 2 PDB
Similar variants
- AGK p.Arg9Pro Uncertain significance ★★ ⚠ same residue
- AGK p.Arg9Ter Pathogenic ★ same residue
- AGK p.Arg9Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
- AGK p.Arg9Gly 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
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-arg9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown