DMBT1 p.Ser1102=
c.3306T>C · rs535950821 · VCV3054471
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0122%, 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 -12 | GERP -2.2 |
| Overall | ||
| CADD | 0.043 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0122%
South Asian · 11/89,930 alleles
Filtering AF
0.00684%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00528%
Overall
0.00199%
32/1,604,916 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0122% | 8,175 |
| East Asian | 0.00905% | 11,048 |
| Remaining individualsnot grpmax-eligible | 0.00804% | 12,438 |
| Admixed American | 0.00172% | 58,068 |
| European (non-Finnish) | 0.000934% | 107,050 |
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.Ser1102=
- Coding
- c.3306T>C
- MANE Select
- NM_001377530
- dbSNP
- rs535950821
- Type
- single nucleotide variant
- Location
- chr10:122600089 (GRCh38)
- Gene constraint
- LOEUF 0.904 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.29 · 6 PDB
- Residue 1102
- a UniProt-annotated variant site (in); the 'disordered' region
Disease context
DMBT1-related disorder
Similar variants
- 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
- DMBT1 p.Arg2060= 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-ser1102 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown