DOCK1 p.Thr1289=
c.3867G>A · VCV4084422
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
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 | GERP -4.7 |
| Overall | ||
| CADD | 0.629 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,178,630 alleles
Overall
6.86e-05%
1/1,457,058 alleles · very rare
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
- DOCK1
- Protein
- p.Thr1289=
- Coding
- c.3867G>A
- MANE Select
- NM_001290223
- Type
- single nucleotide variant
- Location
- chr10:127384849 (GRCh38)
- Gene constraint
- LOEUF 0.637 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.63 · 1 PDB
- Residue 1289
- the docker domain
Similar variants
- DOCK1 p.Pro1783Ser Uncertain significance ★★ ⚠ same type
- DOCK1 p.Ala1185Thr Uncertain significance ★ ⚠ same type
- DOCK1 p.Ala151Thr Uncertain significance ★ ⚠ same type
- DOCK1 p.Ala1578Ser Uncertain significance ★ ⚠ same type
- DOCK1 p.Ala1590Gly Uncertain significance ★ ⚠ same type
- DOCK1 p.Ala1620Val Uncertain significance ★ ⚠ same type
- DOCK1 p.Ala1689Ser Uncertain significance ★ ⚠ same type
- DOCK1 p.Ala280Thr 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/dock1-p-thr1289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown