GNPAT p.Ser333=
c.999A>T · rs755949008 · VCV1593514
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-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 -1.3 | GERP -3.8 |
| Overall | ||
| CADD | 5.487 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,886 alleles
Overall
6.2e-05%
1/1,614,036 alleles · very rare
exomes 1/1,461,698 · genomes 0/152,338 · 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
- GNPAT
- Protein
- p.Ser333=
- Coding
- c.999A>T
- MANE Select
- NM_014236
- dbSNP
- rs755949008
- Type
- single nucleotide variant
- Location
- chr1:231266351 (GRCh38)
- Gene constraint
- LOEUF 0.572 · pLI 0.88 (gnomAD)
- Structure
- AlphaFold pLDDT 88.96
Similar variants
- GNPAT c.569-3T>G Pathogenic ★★ same type
- GNPAT p.Arg163Ter Pathogenic ★★ same type
- GNPAT p.Arg211Cys Likely pathogenic ★★ same type
- GNPAT p.Arg211His Pathogenic ★★ same type
- GNPAT p.Arg335Ter Likely pathogenic ★★ same type
- GNPAT p.Trp386Ter Pathogenic/Likely pathogenic ★★ same type
- GNPAT p.Tyr60Ter Pathogenic/Likely pathogenic ★★ same type
- GNPAT c.924+4C>T 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/gnpat-p-ser333 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown