DAG1 p.His594=
c.1782C>T · rs1553653277 · VCV434894
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, 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 -9.3 | GERP -3.8 |
| Overall | ||
| CADD | 0.457 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,888 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000274%
4/1,461,784 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,888 |
| European (non-Finnish) | 0.000254% | 393,338 |
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
- DAG1
- Protein
- p.His594=
- Coding
- c.1782C>T
- MANE Select
- NM_004393
- dbSNP
- rs1553653277
- Type
- single nucleotide variant
- Location
- chr3:49532293 (GRCh38)
- Gene constraint
- LOEUF 0.298 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 68.44 · 8 PDB
- Residue 594
- a β-strand
Similar variants
- DAG1 p.Ser14Ter Pathogenic ★★ same type
- DAG1 p.Trp110Ter Pathogenic/Likely pathogenic ★★ same type
- DAG1 p.Ala135Ser Uncertain significance ★★ ⚠ same type
- DAG1 p.Ala135Thr Uncertain significance ★★ ⚠ same type
- DAG1 p.Ala279Ser Uncertain significance ★★ ⚠ same type
- DAG1 p.Ala285Thr Uncertain significance ★★ ⚠ same type
- DAG1 p.Ala285Val Uncertain significance ★★ ⚠ same type
- DAG1 p.Ala610Val 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/dag1-p-his594 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown