DDB2 p.Pro19=
c.57C>A · rs779621308 · VCV749111
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0132%, 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 0.33 | GERP 0.41 |
| Overall | ||
| CADD | 10.82 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0132%
South Asian · 12/91,058 alleles
Filtering AF
0.00751%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00593%
Overall
0.000805%
13/1,614,076 alleles · ultra-rare
exomes 13/1,461,886 · genomes 0/152,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0132% | 7,588 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,506 |
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.Pro19=
- Coding
- c.57C>A
- MANE Select
- NM_000107
- dbSNP
- rs779621308
- Type
- single nucleotide variant
- Location
- chr11:47215193 (GRCh38)
- Gene constraint
- LOEUF 0.719 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.69 · 10 PDB
- Residue 19
- the 'disordered' region
Similar variants
- DDB2 c.702+1G>T Pathogenic/Likely pathogenic ★★ same type
- DDB2 p.Arg192Ter Pathogenic/Likely pathogenic ★★ same type
- DDB2 p.Arg273His Pathogenic/Likely pathogenic ★★ same type
- DDB2 p.Arg355Ter Pathogenic ★★ same type
- DDB2 p.Arg332His Uncertain significance ★★ ⚠ same type
- DDB2 p.Cys66Gly Uncertain significance ★★ ⚠ same type
- DDB2 p.Glu178Ala Uncertain significance ★★ ⚠ same type
- DDB2 p.Leu350Pro 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/ddb2-p-pro19 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown