AGPS p.Gln425=
c.1275G>A · rs2468105719 · VCV2770182
Likely benign
Single submitter
Classification
Likely benign
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 carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3 | GERP -0.68, phastCons 1 |
| Overall | ||
| CADD | 6.727 | 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
- AGPS
- Protein
- p.Gln425=
- Coding
- c.1275G>A
- MANE Select
- NM_003659
- dbSNP
- rs2468105719
- Type
- single nucleotide variant
- Location
- chr2:177493189 (GRCh38)
- Gene constraint
- LOEUF 0.408 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.27
Similar variants
- AGPS p.Arg182Ter Pathogenic/Likely pathogenic ★★ same type
- AGPS p.Thr309Ile Likely pathogenic ★★ same type
- AGPS c.1855+6C>A Uncertain significance ★★ same type
- AGPS c.*118A>G Uncertain significance ★★ same type
- AGPS p.Arg265Gln Uncertain significance ★★ ⚠ same type
- AGPS p.Asn649Ser Uncertain significance ★★ ⚠ same type
- AGPS p.Asp28Val Uncertain significance ★★ ⚠ same type
- AGPS p.Asp590His Uncertain significance ★★ ⚠ 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/agps-p-gln425 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown