DMAC1 p.Thr19Ser
c.56C>G · rs368028558 · VCV3082976
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0156%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.022 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.14 | GERP 0.62 |
| Regional constraint | o/e 1.38 | unconstrained · MANE · 1,158 bp · p 1.7e-06 · regional, not allelic |
| Overall | ||
| CADD | 5.297 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0156%
European (non-Finnish) · 183/1,176,646 alleles
Filtering AF
0.0137%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.013%
Overall
0.012%
192/1,602,010 alleles · ultra-rare
exomes 174/1,449,870 · genomes 18/152,140 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0156% | 6,430 |
| Remaining individualsnot grpmax-eligible | 0.0129% | 7,758 |
| African / African-American | 0.00134% | 74,824 |
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
- DMAC1
- Protein
- p.Thr19Ser
- Coding
- c.56C>G
- MANE Select
- NM_033428
- dbSNP
- rs368028558
- Type
- single nucleotide variant
- Location
- chr9:7799679 (GRCh38)
- Gene constraint
- LOEUF 1.842 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 60.00
- Residue 19
- the 'disordered' region
Similar variants
- DMAC1 p.Thr19Ala Likely benign ★ same residue
- DMAC1 p.Ala21Gly Uncertain significance ★ same type
- DMAC1 p.Ala24Gly Uncertain significance ★ same type
- DMAC1 p.Ala30Ser Uncertain significance ★ same type
- DMAC1 p.Ala39Gly Uncertain significance ★ same type
- DMAC1 p.Arg110Cys Uncertain significance ★ same type
- DMAC1 p.Arg110His Uncertain significance ★ same type
- DMAC1 p.Arg42His 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/dmac1-p-thr19ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown