PIDD1 p.Ala908=
c.2724C>G · VCV4910126
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.25e-05%)
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 0.93 | GERP -3.4, phastCons 0.98 |
| Overall | ||
| CADD | 6.081 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.25e-05%
Overall
6.25e-05%
1/1,599,732 alleles · very rare
exomes 1/1,447,350 · genomes 0/152,382 · joint denominator
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.Ala908=
- Coding
- c.2724C>G
- MANE Select
- NM_145886
- Type
- single nucleotide variant
- Location
- chr11:799316 (GRCh38)
- Gene constraint
- LOEUF 1.237 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 50.02 · 2 PDB
- Residue 908
- 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.Ala908Thr Uncertain significance ★ ⚠ same residue
- 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
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-ala908 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown