DOCK6 p.Thr1402=
c.4206G>A · rs764748107 · VCV2724572
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0582%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.61 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.28 | gain · loss 0.02 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -7.4 | GERP -4.9 |
| Overall | ||
| CADD | 1.886 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0582%
South Asian · 53/91,082 alleles
Filtering AF
0.0457%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0412%
Overall
0.00527%
85/1,613,616 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0582% | 1,719 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,821 |
| African / African-American | 0.00267% | 37,453 |
| East Asian | 0.00223% | 44,890 |
| European (non-Finnish) | 0.00212% | 47,195 |
| Admixed American | 0.00167% | 59,992 |
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
- DOCK6
- Protein
- p.Thr1402=
- Coding
- c.4206G>A
- MANE Select
- NM_020812
- dbSNP
- rs764748107
- Type
- single nucleotide variant
- Location
- chr19:11214407 (GRCh38)
- Gene constraint
- LOEUF 0.87 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.78 · 7 PDB
Similar variants
- DOCK6 p.Thr1402Met Benign/Likely benign ★★ ⚠ same residue
- DOCK6 c.4491+1G>A Pathogenic ★★ same type
- DOCK6 c.5939+2T>C Pathogenic ★★ same type
- DOCK6 c.807-1G>A Likely pathogenic ★★ same type
- DOCK6 p.Arg1526Ter Pathogenic/Likely pathogenic ★★ same type
- DOCK6 p.Arg184Ter Pathogenic/Likely pathogenic ★★ same type
- DOCK6 p.Arg488Ter Pathogenic/Likely pathogenic ★★ same type
- DOCK6 p.Gln1188Ter Pathogenic/Likely pathogenic ★★ 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/dock6-p-thr1402 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown