PISD p.Pro221=
c.663G>A · VCV3616564
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.01%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.114 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -6.1 | GERP -8.3 |
| Overall | ||
| CADD | 3.392 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/60,004 alleles
Filtering AF
0.00428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.00192%
31/1,613,930 alleles · very rare
exomes 29/1,461,770 · genomes 2/152,160 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.01% | 10,001 |
| European (non-Finnish) | 0.00203% | 49,167 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
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
- PISD
- Protein
- p.Pro221=
- Coding
- c.663G>A
- MANE Select
- NM_001326411
- Type
- single nucleotide variant
- Location
- chr22:31621368 (GRCh38)
- Gene constraint
- LOEUF 0.979 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.13
Similar variants
- PISD p.Pro221Leu Uncertain significance ★★ same residue
- PISD p.Cys300Tyr Pathogenic/Likely pathogenic ★★ same type
- PISD p.Ala234Val Uncertain significance ★★ ⚠ same type
- PISD p.Ala386Val Uncertain significance ★★ ⚠ same type
- PISD p.Arg125Cys Uncertain significance ★★ ⚠ same type
- PISD p.Arg125His Uncertain significance ★★ ⚠ same type
- PISD p.Arg136His Uncertain significance ★★ ⚠ same type
- PISD p.Arg163Cys 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/pisd-p-pro221 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown