DMBT1 p.Val297=
c.891C>T · VCV4084842
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00892%, 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 -20 | GERP -3.7 |
| Overall | ||
| CADD | 0.51 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00892%
East Asian · 4/44,846 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0018%
Overall
0.000687%
10/1,455,122 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00892% | 11,212 |
| Admixed American | 0.00167% | 59,998 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,288 |
| African / African-American | 0.00133% | 74,978 |
| European (non-Finnish) | 0.000256% | 391,278 |
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.Val297=
- Coding
- c.891C>T
- MANE Select
- NM_001377530
- Type
- single nucleotide variant
- Location
- chr10:122579789 (GRCh38)
- Gene constraint
- LOEUF 0.904 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.29 · 6 PDB
- Residue 297
- the srcr 2 domain; a disulfide bond
Similar variants
- DMBT1 p.Asp696Val Uncertain significance ★★ ⚠ same type
- 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.Asp696= Likely benign ★★ same type
- DMBT1 p.Gln1656Arg 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-val297 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown