PIGT p.Pro38=
c.114G>T · VCV4945143
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00205%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.021 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.032 | GERP -4.9, phastCons 0.095 |
| Overall | ||
| CADD | 10.9 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00205%
European (non-Finnish) · 24/1,171,110 alleles
Filtering AF
0.00139%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00117%
Overall
0.0015%
24/1,594,766 alleles · very rare
exomes 23/1,442,538 · genomes 1/152,228 · joint denominator
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
- PIGT
- Protein
- p.Pro38=
- Coding
- c.114G>T
- MANE Select
- NM_015937
- Type
- single nucleotide variant
- Location
- chr20:45416270 (GRCh38)
- Gene constraint
- LOEUF 1.084 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.71 · 4 PDB
- Residue 38
- a β-strand
Similar variants
- PIGT p.Pro38Leu Uncertain significance ★★ same residue
- PIGT c.188-2A>G Pathogenic/Likely pathogenic ★★ same type
- PIGT c.494-2A>G Pathogenic ★★ same type
- PIGT p.Arg172Cys Pathogenic/Likely pathogenic ★★ same type
- PIGT p.Arg266Ter Pathogenic/Likely pathogenic ★★ same type
- PIGT p.Arg330Ter Pathogenic ★★ same type
- PIGT p.Arg448Trp Pathogenic/Likely pathogenic ★★ same type
- PIGT p.Glu237Gln 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/pigt-p-pro38 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown