PIGT p.Pro577=
c.1731A>G · VCV4945156
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, 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 -8.8 | GERP -4.8 |
| Overall | ||
| CADD | 0.159 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,830 alleles
Filtering AF
0.000365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000137%
Overall
0.000186%
3/1,611,770 alleles · very rare
exomes 3/1,460,388 · genomes 0/151,382 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,830 |
| South Asian | 0.0022% | 45,491 |
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.Pro577=
- Coding
- c.1731A>G
- MANE Select
- NM_015937
- Type
- single nucleotide variant
- Location
- chr20:45425820 (GRCh38)
- Gene constraint
- LOEUF 1.084 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.71 · 4 PDB
- Residue 577
- a UniProt-annotated variant site (in mcahs3; loss of function in gpi-anchor attachment to protein); a UniProt-annotated variant site (in mcahs3)
Similar variants
- PIGT p.Pro577Ala Uncertain significance ★ ⚠ same residue
- PIGT p.Pro577Gln Uncertain significance ★ ⚠ same residue
- PIGT p.Pro577Leu Uncertain significance ★ ⚠ same residue
- PIGT p.Pro577fs 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
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-pro577 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown