DBNDD2 p.Trp27Arg
c.79T>C · VCV3499782
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0452%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.086 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 2.2, phastCons 1 |
| Overall | ||
| CADD | 20.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0452%
African / African-American · 33/73,060 alleles
Filtering AF
0.033%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0289%
Overall
0.00277%
43/1,551,170 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0452% | 2,214 |
| Remaining individualsnot grpmax-eligible | 0.00997% | 10,032 |
| Admixed American | 0.00784% | 12,752 |
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
- DBNDD2
- Protein
- p.Trp27Arg
- Coding
- c.79T>C
- MANE Select
- NM_001048225
- Type
- single nucleotide variant
- Location
- chr20:45408240 (GRCh38)
- Gene constraint
- LOEUF 1.061 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 60.09
- Residue 27
- the 'disordered' region
Similar variants
- DBNDD2 c.78G>T Uncertain significance ★ same type
- DBNDD2 c.95C>A Uncertain significance ★ same type
- DBNDD2 c.-146C>T Uncertain significance ★ same type
- DBNDD2 c.-15C>A Uncertain significance ★ ⚠ same type
- DBNDD2 c.-29G>T Uncertain significance ★ ⚠ same type
- DBNDD2 c.-32C>T Uncertain significance ★ ⚠ same type
- DBNDD2 c.-5C>A Uncertain significance ★ ⚠ same type
- DBNDD2 c.-5C>T 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/dbndd2-p-trp27arg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown