DBR1 p.Asp504=
c.1512C>T · rs142272005 · VCV2072959
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.181%, mid)
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 3.4 | phastCons 1 |
| Overall | ||
| CADD | 8.486 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.181%
Middle Eastern · 11/6,062 alleles
Filtering AF
0.102%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0787%
Overall
0.0185%
299/1,614,062 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.181% | 551 |
| European (non-Finnish) | 0.0225% | 4,436 |
| Remaining individualsnot grpmax-eligible | 0.0208% | 4,808 |
| Admixed American | 0.00667% | 14,998 |
| South Asian | 0.00439% | 22,770 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
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
- DBR1
- Protein
- p.Asp504=
- Coding
- c.1512C>T
- MANE Select
- NM_016216
- dbSNP
- rs142272005
- Type
- single nucleotide variant
- Location
- chr3:138162012 (GRCh38)
- Gene constraint
- LOEUF 0.841 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.04
- Residue 504
- the 'disordered' region; a UniProt-annotated variant site (in iiae11; loss of protein expression)
Similar variants
- DBR1 c.489+5G>A Uncertain significance ★★ same type
- DBR1 p.Ala233Thr Uncertain significance ★★ ⚠ same type
- DBR1 p.Ala443Thr Uncertain significance ★★ ⚠ same type
- DBR1 p.Ala458Asp Uncertain significance ★★ ⚠ same type
- DBR1 p.Arg197Gln Uncertain significance ★★ ⚠ same type
- DBR1 p.Arg197Ter Uncertain significance ★★ same type
- DBR1 p.Arg527Ser Uncertain significance ★★ ⚠ same type
- DBR1 p.Asn405His 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/dbr1-p-asp504 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown