PIGP p.Pro37=
c.111T>G · rs1025041839 · VCV2067770
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00191%, nfe)
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 0.21 | GERP -3.6, phastCons 0.31 |
| Overall | ||
| CADD | 9.059 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00191%
European (non-Finnish) · 22/1,154,628 alleles
Filtering AF
0.00125%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00106%
Overall
0.00146%
23/1,570,258 alleles · very rare
exomes 23/1,417,966 · genomes 0/152,292 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00191% | 52,483 |
| African / African-American | 0.00135% | 73,834 |
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
- PIGP
- Protein
- p.Pro37=
- Coding
- c.111T>G
- MANE Select
- NM_153682
- dbSNP
- rs1025041839
- Type
- single nucleotide variant
- Location
- chr21:37069596 (GRCh38)
- Gene constraint
- LOEUF 1.937 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.42
Similar variants
- PIGP p.Pro37Thr Uncertain significance ★ ⚠ same residue
- PIGP p.Met1Thr Pathogenic/Likely pathogenic ★★ same type
- PIGP c.-12G>A Uncertain significance ★★ ⚠ same type
- PIGP c.-20T>G Uncertain significance ★★ ⚠ same type
- PIGP c.-8C>T Uncertain significance ★★ ⚠ same type
- PIGP p.Ala95Glu Uncertain significance ★★ ⚠ same type
- PIGP p.Gln98Ter Uncertain significance ★★ same type
- PIGP p.Ile108Phe 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/pigp-p-pro37 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown