DMBT1 p.Arg2060=
c.6180T>A · rs551305593 · VCV3044693
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.391%, sas)
Conditions
1
DMBT1-related disorder
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 -20 | GERP -3.8 |
| Overall | ||
| CADD | 0.225 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.391%
South Asian · 356/91,070 alleles
Filtering AF
0.357%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.344%
Overall
0.0232%
375/1,614,008 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.391% | 256 |
| Remaining individualsnot grpmax-eligible | 0.0224% | 4,463 |
| African / African-American | 0.00133% | 75,044 |
| European (non-Finnish) | 0.000339% | 294,976 |
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
- DMBT1
- Protein
- p.Arg2060=
- Coding
- c.6180T>A
- MANE Select
- NM_001377530
- dbSNP
- rs551305593
- Type
- single nucleotide variant
- Location
- chr10:122631115 (GRCh38)
- Gene constraint
- LOEUF 0.904 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.29 · 6 PDB
- Residue 2060
- the cub 2 domain; a disulfide bond
Disease context
DMBT1-related disorder
Similar variants
- DMBT1 p.Arg2060His Uncertain significance ★ ⚠ same residue
- DMBT1 c.1033+10C>T Likely benign same condition
- DMBT1 c.1459+7A>T Likely benign same condition
- DMBT1 c.6026-9G>C Benign same condition
- DMBT1 c.6548+10C>T Likely benign same condition
- DMBT1 p.Ala268Val Benign same condition
- DMBT1 p.Arg1098Gln Benign same condition
- DMBT1 p.Arg1626His Likely benign 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/dmbt1-p-arg2060 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown