DDB2 p.Thr406=
c.1218G>A · rs1470480918 · VCV3026314
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 -2.9 | GERP -4.6 |
| Overall | ||
| CADD | 4.82 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,860 alleles
Filtering AF
7.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000434%
7/1,611,192 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,860 |
| African / African-American | 0.00134% | 74,896 |
| South Asian | 0.00111% | 90,388 |
| European (non-Finnish) | 0.000339% | 294,679 |
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.Thr406=
- Coding
- c.1218G>A
- MANE Select
- NM_000107
- dbSNP
- rs1470480918
- Type
- single nucleotide variant
- Location
- chr11:47238167 (GRCh38)
- Gene constraint
- LOEUF 0.719 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 83.69 · 10 PDB
Similar variants
- DDB2 p.Thr406Met Uncertain significance ★★ ⚠ same residue
- 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
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-thr406 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown