GNPAT p.Arg210=
c.628C>A · rs199523352 · VCV1652839
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0557%, eas)
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 2.8 | GERP 1.3, phastCons 1 |
| Overall | ||
| CADD | 11.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0557%
East Asian · 25/44,844 alleles
Filtering AF
0.0387%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.033%
Overall
0.00211%
34/1,609,420 alleles · ultra-rare
exomes 31/1,457,232 · genomes 3/152,188 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0557% | 1,794 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,171 |
| European (non-Finnish) | 0.000595% | 167,976 |
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.Arg210=
- Coding
- c.628C>A
- MANE Select
- NM_014236
- dbSNP
- rs199523352
- Type
- single nucleotide variant
- Location
- chr1:231265352 (GRCh38)
- Gene constraint
- LOEUF 0.572 · pLI 0.88 (gnomAD)
- Structure
- AlphaFold pLDDT 88.96
Similar variants
- GNPAT p.Arg210Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
- 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
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-arg210 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown