PIGO p.Arg970=
c.2910G>A · rs1171844461 · VCV508393
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00534%, afr)
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 0.6 | GERP 0.5, phastCons 0.42 |
| Overall | ||
| CADD | 5.609 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00534%
African / African-American · 4/74,928 alleles
Filtering AF
0.00175%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00104%
Overall
0.00062%
10/1,614,086 alleles · very rare
exomes 4/1,461,872 · genomes 6/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00534% | 18,732 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
| European (non-Finnish) | 0.000424% | 236,010 |
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
- PIGO
- Protein
- p.Arg970=
- Coding
- c.2910G>A
- MANE Select
- NM_032634
- dbSNP
- rs1171844461
- Type
- single nucleotide variant
- Location
- chr9:35090225 (GRCh38)
- Gene constraint
- LOEUF 0.89 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.57
- Residue 970
- a UniProt-annotated variant site (in hpmrs2)
Similar variants
- PIGO p.Arg970Gln Uncertain significance ★ ⚠ same residue
- PIGO p.Arg970Trp Conflicting classifications of pathogenicity ★ ⚠ same residue
- PIGO c.2648-1G>A Likely pathogenic ★★ same type
- PIGO c.3069+2T>C Likely pathogenic ★★ same type
- PIGO c.3069+5G>A Pathogenic/Likely pathogenic ★★ same type
- PIGO p.Arg119Trp Likely pathogenic ★★ ⚠ same type
- PIGO p.Arg122Ter Pathogenic/Likely pathogenic ★★ same type
- PIGO p.Arg376Ter 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/pigo-p-arg970 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown