Is DDB2 p.Pro290= (c.870T>C) pathogenic?

DDB2 p.Pro290= (c.870T>C) is classified Likely benign in DDB2 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-12-28). Very rare (popmax 0.000339%, nfe); Associated with xeroderma pigmentosum.

What condition is associated with DDB2 p.Pro290= (c.870T>C)?

DDB2 p.Pro290= (c.870T>C) is associated with xeroderma pigmentosum (ClinVar).

How common is DDB2 p.Pro290= (c.870T>C) in the general population?

DDB2 p.Pro290= (c.870T>C) is very rare (popmax 0.000339%, nfe) (gnomAD).

How is Xeroderma pigmentosum inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

DDB2 p.Pro290=

c.870T>C · rs376783024 · VCV1692153

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.000339%, nfe)

Conditions

xeroderma pigmentosum

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 -0.26	GERP -2.1, phastCons 0.52
Overall
CADD	9.602	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000339% European (non-Finnish) · 4/1,180,044 alleles

Filtering AF 7.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.00626% 101/1,614,100 alleles · very rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.294%	340
Remaining individualsnot grpmax-eligible	0.0144%	6,943
Finnishnot grpmax-eligible	0.00156%	64,042
European (non-Finnish)grpmax	0.000339%	295,011

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: DDB2
Protein: p.Pro290=
Coding: c.870T>C
MANE Select: NM_000107
dbSNP: rs376783024
Type: single nucleotide variant
Location: chr11:47234924 (GRCh38)
Gene constraint: LOEUF 0.719 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 83.69 · 10 PDB

Full DDB2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

xeroderma pigmentosum — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Xeroderma pigmentosum (Orphanet):

Inheritance: Autosomal recessive
Onset: All ages
Prevalence: 1-9 / 1 000 000 (United States)

Similar variants

DDB2 p.Pro290Leu Uncertain significance ★ ⚠ same residue
DDB2 p.Cys66Gly Uncertain significance ★★ ⚠ same condition
DDB2 p.Met215Thr Likely benign ★★ same condition
DDB2 c.127+5T>G Conflicting classifications of pathogenicity ★ same condition
DDB2 c.264+8A>G Conflicting classifications of pathogenicity ★ same condition
DDB2 c.603-4C>G Uncertain significance ★ same condition
DDB2 c.702+5G>A Uncertain significance ★ same condition
DDB2 p.Ala410Thr Conflicting classifications of pathogenicity ★ ⚠ 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/ddb2-p-pro290 (accessed [today's date]).

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