AGPS p.Ala17=
c.51G>T · rs1055974652 · VCV1100396
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00165%, nfe)
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 1.2 | GERP 0.64, phastCons 0.99 |
| Overall | ||
| CADD | 8.066 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00165%
European (non-Finnish) · 19/1,152,910 alleles
Filtering AF
0.00105%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000849%
Overall
0.00123%
19/1,548,114 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
- AGPS
- Protein
- p.Ala17=
- Coding
- c.51G>T
- MANE Select
- NM_003659
- dbSNP
- rs1055974652
- Type
- single nucleotide variant
- Location
- chr2:177392840 (GRCh38)
- Gene constraint
- LOEUF 0.408 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 89.27
- Residue 17
- the 'disordered' region
Similar variants
- AGPS p.Ala17_Ser18dup Uncertain significance ★★ same residue
- AGPS p.Ala17_Ser18insThrGlyLeuGlyAlaGlyAla Uncertain significance ★ same residue
- 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
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-ala17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown