PGAP2 p.His203=
c.609C>T · rs147354096 · VCV2712857
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0802%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.238 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -8.1 | GERP -3.2 |
| Overall | ||
| CADD | 0.069 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0802%
East Asian · 36/44,888 alleles
Filtering AF
0.0595%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0524%
Overall
0.0255%
412/1,614,204 alleles · ultra-rare
exomes 380/1,461,886 · genomes 32/152,318 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0802% | 1,247 |
| Admixed American | 0.0417% | 2,401 |
| European (non-Finnish) | 0.0274% | 3,653 |
| Remaining individualsnot grpmax-eligible | 0.0208% | 4,808 |
| African / African-American | 0.0107% | 9,381 |
| South Asian | 0.00769% | 13,012 |
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
- PGAP2
- Protein
- p.His203=
- Coding
- c.609C>T
- MANE Select
- NM_014489
- dbSNP
- rs147354096
- Type
- single nucleotide variant
- Location
- chr11:3824277 (GRCh38)
- Gene constraint
- LOEUF 0.871 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.00
Similar variants
- PGAP2 p.Ala127Val Likely pathogenic ★★ same type
- PGAP2 p.Arg238Pro Pathogenic/Likely pathogenic ★★ ⚠ same type
- PGAP2 p.Thr294Met Likely pathogenic ★★ same type
- PGAP2 c.602-3C>T Uncertain significance ★★ same type
- PGAP2 p.Ala187Thr Uncertain significance ★★ ⚠ same type
- PGAP2 p.Ala33Thr Uncertain significance ★★ ⚠ same type
- PGAP2 p.Arg238Cys Uncertain significance ★★ ⚠ same type
- PGAP2 p.Asn205Lys 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/pgap2-p-his203 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown