GNPAT p.Pro492=
c.1476A>G · rs113006651 · VCV1134723
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0253%, 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 -9.7 | GERP -4.5 |
| Overall | ||
| CADD | 0.075 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0253%
African / African-American · 19/75,032 alleles
Filtering AF
0.0165%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0137%
Overall
0.00211%
34/1,614,086 alleles · ultra-rare
exomes 28/1,461,788 · genomes 6/152,298 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0253% | 3,949 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,209 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.00167% | 60,032 |
| South Asian | 0.0011% | 91,082 |
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.Pro492=
- Coding
- c.1476A>G
- MANE Select
- NM_014236
- dbSNP
- rs113006651
- Type
- single nucleotide variant
- Location
- chr1:231270954 (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-pro492 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown