PIGP p.Ser22=
c.66C>T · rs908030943 · VCV1612196
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00801%, afr)
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 4 | GERP 0.7, phastCons 1 |
| Overall | ||
| CADD | 12.93 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00801%
African / African-American · 6/74,940 alleles
Filtering AF
0.00347%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00228%
Overall
0.00062%
10/1,614,118 alleles · very rare
exomes 3/1,461,866 · genomes 7/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00801% | 12,490 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,828 |
| Admixed American | 0.00167% | 60,014 |
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.Ser22=
- Coding
- c.66C>T
- MANE Select
- NM_153682
- dbSNP
- rs908030943
- Type
- single nucleotide variant
- Location
- chr21:37072450 (GRCh38)
- Gene constraint
- LOEUF 1.937 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.42
Similar variants
- 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
- PIGP p.Ile28Arg 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-ser22 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown