PGAP3 p.Ala2=
c.6C>T · rs199645746 · VCV2413667
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0485%, 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 -2.4 | GERP -5.3 |
| Overall | ||
| CADD | 7.35 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0485%
East Asian · 17/35,034 alleles
Filtering AF
0.0309%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0253%
Overall
0.00334%
47/1,406,556 alleles · ultra-rare
exomes 38/1,254,214 · genomes 9/152,342 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0485% | 2,061 |
| South Asian | 0.0365% | 2,737 |
| Remaining individualsnot grpmax-eligible | 0.00757% | 13,209 |
| African / African-American | 0.00147% | 68,126 |
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
- PGAP3
- Protein
- p.Ala2=
- Coding
- c.6C>T
- MANE Select
- NM_033419
- dbSNP
- rs199645746
- Type
- single nucleotide variant
- Location
- chr17:39688009 (GRCh38)
- Gene constraint
- LOEUF 1.147 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.17
Similar variants
- PGAP3 c.558-10G>A Pathogenic/Likely pathogenic ★★ same type
- PGAP3 c.694+1G>A Pathogenic ★★ same type
- PGAP3 p.Asp305Gly Pathogenic/Likely pathogenic ★★ same type
- PGAP3 p.Gln89Ter Pathogenic ★★ same type
- PGAP3 p.Glu37Ter Pathogenic ★★ same type
- PGAP3 p.His284Arg Pathogenic/Likely pathogenic ★★ ⚠ same type
- PGAP3 p.His284Tyr Pathogenic/Likely pathogenic ★★ same type
- PGAP3 p.Pro105Gln 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/pgap3-p-ala2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown