GNPTG p.Ala3=
c.9G>C · rs763764801 · VCV1635862
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 9.62e-05%, 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 -0.97 | GERP -1 |
| Overall | ||
| CADD | 6.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.62e-05%
European (non-Finnish) · 1/1,039,378 alleles
Overall
7.57e-05%
1/1,320,438 alleles · very rare
exomes 1/1,168,698 · genomes 0/151,740 · joint denominator
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
- GNPTG
- Protein
- p.Ala3=
- Coding
- c.9G>C
- MANE Select
- NM_032520
- dbSNP
- rs763764801
- Type
- single nucleotide variant
- Location
- chr16:1351974 (GRCh38)
- Gene constraint
- LOEUF 1.369 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.63
Similar variants
- GNPTG p.Ala3Val Uncertain significance ★★ ⚠ same residue
- GNPTG p.Ala3Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
- GNPTG p.Ala3fs Pathogenic ★ same residue
- GNPTG p.Ala3del Uncertain significance ★ same residue
- GNPTG c.179-1G>A Likely pathogenic ★★ same type
- GNPTG c.233+1G>A Pathogenic/Likely pathogenic ★★ same type
- GNPTG c.234-1G>A Pathogenic/Likely pathogenic ★★ same type
- GNPTG c.234-1G>C 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/gnptg-p-ala3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown