DMBX1 p.Ser279=
c.837G>A · rs747278905 · VCV3034832
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0178%, eas)
Conditions
1
DMBX1-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 -10 | GERP -5.3 |
| Overall | ||
| CADD | 0.068 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0178%
East Asian · 8/44,872 alleles
Filtering AF
0.00884%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00641%
Overall
0.0013%
21/1,613,886 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0178% | 5,609 |
| Admixed American | 0.00833% | 11,999 |
| South Asian | 0.00439% | 22,772 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,241 |
| European (non-Finnish) | 0.000169% | 589,988 |
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
- DMBX1
- Protein
- p.Ser279=
- Coding
- c.837G>A
- MANE Select
- NM_172225
- dbSNP
- rs747278905
- Type
- single nucleotide variant
- Location
- chr1:46512197 (GRCh38)
- Gene constraint
- LOEUF 0.407 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.71
Disease context
DMBX1-related disorder
Similar variants
- DMBX1 p.Ser279Leu Uncertain significance ★ ⚠ same residue
- DMBX1 p.Ala148= Benign same condition
- DMBX1 p.Ala200Pro Benign same condition
- DMBX1 p.Glu185= Likely benign same condition
- DMBX1 p.Gly285Ala Likely benign same condition
- DMBX1 p.Leu335= Likely benign same condition
- DMBX1 c.155-10A>T Uncertain significance ★ ⚠ same type
- DMBX1 p.Ala213Val 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/dmbx1-p-ser279 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown