PIDD1 p.Pro894=
c.2682C>G · rs11820580 · VCV768409
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 9.54%, afr) — too common for a highly-penetrant pathogenic allele
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 -9.2 | GERP -3 |
| Overall | ||
| CADD | 0.032 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.54%
African / African-American · 7,163/75,048 alleles
Filtering AF
9.36%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9.28%
Overall
0.516%
8,312/1,611,002 alleles · common
exomes 4,128/1,458,656 · genomes 4,184/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 9.54% | 10 |
| Middle Eastern | 0.793% | 126 |
| Admixed American | 0.724% | 138 |
| Remaining individualsnot grpmax-eligible | 0.713% | 140 |
| South Asian | 0.0242% | 4,138 |
| European (non-Finnish) | 0.0169% | 5,928 |
| East Asian | 0.00223% | 44,860 |
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
- PIDD1
- Protein
- p.Pro894=
- Coding
- c.2682C>G
- MANE Select
- NM_145886
- dbSNP
- rs11820580
- Type
- single nucleotide variant
- Location
- chr11:799358 (GRCh38)
- Gene constraint
- LOEUF 1.237 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.02 · 2 PDB
- Residue 894
- the 'disordered' region; a UniProt-annotated variant site (in mrt75); a UniProt-annotated variant site (in mrt75; loss of interaction with cradd; loss of activation of casp2 protein)
Similar variants
- PIDD1 p.Arg637Ter Pathogenic/Likely pathogenic ★★ same type
- PIDD1 p.Arg862Trp Pathogenic ★★ same type
- PIDD1 p.Arg551Cys Uncertain significance ★★ ⚠ same type
- PIDD1 p.Arg605Gln Uncertain significance ★★ ⚠ same type
- PIDD1 p.Arg725Cys Uncertain significance ★★ same type
- PIDD1 p.Arg742Ser Uncertain significance ★★ ⚠ same type
- PIDD1 p.Arg821Trp Uncertain significance ★★ ⚠ same type
- PIDD1 p.Arg842His 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/pidd1-p-pro894 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown