GNPAT p.Ser359=
c.1077T>G · rs1288743848 · VCV2904035
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00268%, afr)
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 -13 | GERP -4.5 |
| Overall | ||
| CADD | 0.023 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00268%
African / African-American · 2/74,558 alleles
Filtering AF
0.000622%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00048%
Overall
0.000939%
15/1,597,886 alleles · very rare
exomes 12/1,445,716 · genomes 3/152,170 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00268% | 37,279 |
| European (non-Finnish) | 0.00112% | 89,641 |
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.Ser359=
- Coding
- c.1077T>G
- MANE Select
- NM_014236
- dbSNP
- rs1288743848
- Type
- single nucleotide variant
- Location
- chr1:231267701 (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-ser359 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown