DMBT1 p.Asp696=
c.2088T>C · rs764944464 · VCV2640932
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0196%, 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 -20 | GERP -3.7 |
| Overall | ||
| CADD | 0.218 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0196%
South Asian · 17/86,956 alleles
Filtering AF
0.0124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0102%
Overall
0.00151%
24/1,588,524 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0196% | 5,115 |
| Middle Eastern | 0.0165% | 6,044 |
| Admixed American | 0.00168% | 59,544 |
| European (non-Finnish) | 0.000429% | 233,157 |
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.Asp696=
- Coding
- c.2088T>C
- MANE Select
- NM_001377530
- dbSNP
- rs764944464
- Type
- single nucleotide variant
- Location
- chr10:122589248 (GRCh38)
- Gene constraint
- LOEUF 0.904 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.29 · 6 PDB
- Residue 696
- a disulfide bond; the srcr 5 domain
Similar variants
- DMBT1 p.Asp696Val Uncertain significance ★★ ⚠ same residue
- DMBT1 p.His805Asn Uncertain significance ★★ ⚠ same type
- DMBT1 p.Arg670Cys Benign ★★ ⚠ same type
- DMBT1 p.Asp1796Glu Benign ★★ ⚠ same type
- DMBT1 p.Asp635Asn Benign ★★ ⚠ same type
- DMBT1 p.Asp668Asn Benign ★★ same type
- DMBT1 p.Gln1656Arg Benign ★★ same type
- DMBT1 p.Leu1759Ser Benign/Likely benign ★★ 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/dmbt1-p-asp696 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown