PIDD1 p.Ala152=
c.456G>A · VCV3770892
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00659%, sas)
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 -3.9 | GERP -3.4 |
| Overall | ||
| CADD | 0.685 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00659%
South Asian · 6/91,080 alleles
Filtering AF
0.00286%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00195%
Overall
0.00105%
17/1,613,860 alleles · very rare
exomes 17/1,461,598 · genomes 0/152,262 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00659% | 15,180 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,502 |
| African / African-American | 0.00133% | 75,042 |
| European (non-Finnish) | 0.000763% | 131,110 |
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.Ala152=
- Coding
- c.456G>A
- MANE Select
- NM_145886
- Type
- single nucleotide variant
- Location
- chr11:803427 (GRCh38)
- Gene constraint
- LOEUF 1.237 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.02 · 2 PDB
- Residue 152
- the 'disordered' region
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-ala152 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown