Is PIDD1 p.Asp301= (c.903C>T) pathogenic?

PIDD1 p.Asp301= (c.903C>T) is classified Likely benign in PIDD1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-04-26). Ultra-rare (popmax 0.0331%, mid); Associated with PIDD1-related disorder.

What condition is associated with PIDD1 p.Asp301= (c.903C>T)?

PIDD1 p.Asp301= (c.903C>T) is associated with PIDD1-related disorder (ClinVar).

How common is PIDD1 p.Asp301= (c.903C>T) in the general population?

PIDD1 p.Asp301= (c.903C>T) is ultra-rare (popmax 0.0331%, mid) (gnomAD).

PIDD1 p.Asp301=

c.903C>T · rs373164089 · VCV3045156

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0331%, mid)

Conditions

PIDD1-related disorder

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 -1.3	GERP -2.9
Overall
CADD	3.09	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0331% Middle Eastern · 2/6,050 alleles

Filtering AF 0.00583% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00313%

Overall 0.00261% 42/1,610,744 alleles · ultra-rare exomes 39/1,458,436 · genomes 3/152,308 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0331%	3,025
South Asian	0.00883%	11,329
Remaining individualsnot grpmax-eligible	0.00321%	31,195
European (non-Finnish)	0.00238%	42,092
Finnishnot grpmax-eligible	0.00158%	63,102
African / African-American	0.00133%	75,024

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.Asp301=
Coding: c.903C>T
MANE Select: NM_145886
dbSNP: rs373164089
Type: single nucleotide variant
Location: chr11:802698 (GRCh38)
Gene constraint: LOEUF 1.237 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 50.02 · 2 PDB

Full PIDD1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

PIDD1-related disorder

Similar variants

PIDD1 p.Glu734Lys Uncertain significance ★★ ⚠ same condition
PIDD1 c.2042-2A>G Conflicting classifications of pathogenicity ★ same condition
PIDD1 p.Gln391= Conflicting classifications of pathogenicity ★ same condition
PIDD1 c.2475-10C>T Likely benign same condition
PIDD1 c.710-4G>A Likely benign same condition
PIDD1 p.Ala670= Likely benign same condition
PIDD1 p.Arg549Leu Likely benign same condition
PIDD1 p.Arg652Trp Benign same condition

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-asp301 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown