DACH1 p.Ser153=
c.459T>C · VCV3904906
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.013%, sas)
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 -0.066 | GERP -3.6, phastCons 0.99 |
| Overall | ||
| CADD | 4.504 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.013%
South Asian · 11/84,326 alleles
Filtering AF
0.00775%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00724%
Overall
0.00824%
127/1,541,618 alleles · ultra-rare
exomes 114/1,390,582 · genomes 13/151,036 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.013% | 7,666 |
| European (non-Finnish) | 0.0092% | 10,865 |
| Admixed American | 0.00587% | 17,021 |
| Remaining individualsnot grpmax-eligible | 0.00503% | 19,878 |
| African / African-American | 0.00412% | 24,271 |
| Finnishnot grpmax-eligible | 0.00347% | 28,805 |
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
- DACH1
- Protein
- p.Ser153=
- Coding
- c.459T>C
- MANE Select
- NM_080759
- Type
- single nucleotide variant
- Location
- chr13:71866311 (GRCh38)
- Gene constraint
- LOEUF 0.371 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 58.74 · 1 PDB
- Residue 153
- the 'disordered' region
Similar variants
- DACH1 p.Ser153Arg Uncertain significance ★ ⚠ same residue
- DACH1 p.Val375= Benign ★★ same type
- DACH1 c.1722+6C>T Conflicting classifications of pathogenicity ★ same type
- DACH1 p.Ala109Val Uncertain significance ★ ⚠ same type
- DACH1 p.Ala36Glu Uncertain significance ★ ⚠ same type
- DACH1 p.Ala36Val Uncertain significance ★ ⚠ same type
- DACH1 p.Ala418Thr Uncertain significance ★ ⚠ same type
- DACH1 p.Ala533Thr 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/dach1-p-ser153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown