DACT1 p.Lys102=
c.306G>A · rs199621547 · VCV725177
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,353,652)
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 0.046, phastCons 1 |
| Overall | ||
| CADD | 14.66 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,353,652). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- DACT1
- Protein
- p.Lys102=
- Coding
- c.306G>A
- MANE Select
- NM_001079520
- dbSNP
- rs199621547
- Type
- single nucleotide variant
- Location
- chr14:58638508 (GRCh38)
- Gene constraint
- LOEUF 0.703 · pLI 0.17 (gnomAD)
- Structure
- AlphaFold pLDDT 50.95
- Residue 102
- the 'required for self-association' region
Similar variants
- DACT1 p.Glu451Asp Uncertain significance ★★ ⚠ same type
- DACT1 c.635-121T>C Likely benign ★★ same type
- DACT1 p.Ala427Val Benign ★★ same type
- DACT1 p.Ala500= Benign ★★ same type
- DACT1 p.Asp409Asn Benign ★★ same type
- DACT1 p.Glu257Lys Benign/Likely benign ★★ same type
- DACT1 p.Glu49= Likely benign ★★ same type
- DACT1 p.Gly660Ser Benign ★★ 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/dact1-p-lys102 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown