PIDD1 p.Asp284=
c.852C>T · VCV4821447
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.314%, mid)
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 -4.1 | GERP -2.9 |
| Overall | ||
| CADD | 4.735 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.314%
Middle Eastern · 19/6,058 alleles
Filtering AF
0.221%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.209%
Overall
0.0311%
501/1,611,112 alleles · rare
exomes 379/1,458,814 · genomes 122/152,298 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.314% | 319 |
| Admixed American | 0.254% | 393 |
| African / African-American | 0.237% | 421 |
| Remaining individualsnot grpmax-eligible | 0.0673% | 1,486 |
| South Asian | 0.011% | 9,067 |
| European (non-Finnish) | 0.00814% | 12,283 |
| East Asian | 0.00669% | 14,939 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,546 |
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.Asp284=
- Coding
- c.852C>T
- MANE Select
- NM_145886
- Type
- single nucleotide variant
- Location
- chr11:802749 (GRCh38)
- Gene constraint
- LOEUF 1.237 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.02 · 2 PDB
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-asp284 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown