DOCK6 c.2160+4C>T
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0226%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +4 | donor splice region (+4, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.7 | GERP -4.7 |
| Non-coding constraint | Z 5.24 | 1 kb window · o/e 0.69 · regional · uncalibrated |
| Overall | ||
| CADD | 10.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0226%
South Asian · 19/84,112 alleles
Filtering AF
0.0147%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0123%
Overall
0.00232%
36/1,552,316 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0226% | 4,427 |
| Admixed American | 0.00587% | 17,024 |
| Remaining individualsnot grpmax-eligible | 0.00333% | 30,074 |
| East Asian | 0.00244% | 41,030 |
| European (non-Finnish) | 0.000958% | 104,345 |
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
- Coding
- c.2160+4C>T
- MANE Select
- NM_020812
- dbSNP
- rs1024702531
- Type
- single nucleotide variant
- Location
- chr19:11236789 (GRCh38)
- Gene constraint
- LOEUF 0.87 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.78 · 7 PDB
Similar variants
- 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
- DOCK6 p.Glu1494Ter 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-c-2160-plus-4c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown