PGAP3 p.Phe142=
c.426C>T · VCV3605814
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00993%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.46 | GERP -4.4, phastCons 0.001 |
| Overall | ||
| CADD | 12.57 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00993%
South Asian · 9/90,602 alleles
Filtering AF
0.00516%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00377%
Overall
0.00124%
20/1,610,128 alleles · very rare
exomes 18/1,457,878 · genomes 2/152,250 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00993% | 10,067 |
| East Asian | 0.00224% | 44,676 |
| Admixed American | 0.00169% | 59,208 |
| African / African-American | 0.00134% | 74,684 |
| European (non-Finnish) | 0.000679% | 147,296 |
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.Phe142=
- Coding
- c.426C>T
- MANE Select
- NM_033419
- Type
- single nucleotide variant
- Location
- chr17:39684603 (GRCh38)
- Gene constraint
- LOEUF 1.147 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 93.17
Similar variants
- PER1 p.Leu142Val Uncertain significance ★ ⚠ same residue
- 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
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-phe142 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown