DOCK6 c.1643+101G>A
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.96%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +101 | deep intronic (+101 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.7 | GERP -2.1 |
| Non-coding constraint | Z 3.08 | 1 kb window · o/e 0.78 · regional · uncalibrated |
| Overall | ||
| CADD | 0.053 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.96%
African / African-American · 1,367/69,610 alleles
Filtering AF
1.88%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.84%
Overall
0.108%
1,544/1,434,076 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.96% | 51 |
| Admixed American | 0.145% | 692 |
| Remaining individualsnot grpmax-eligible | 0.135% | 738 |
| Middle Eastern | 0.0751% | 1,331 |
| South Asian | 0.00402% | 24,903 |
| European (non-Finnish) | 0.00356% | 28,075 |
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.1643+101G>A
- MANE Select
- NM_020812
- dbSNP
- rs112103971
- Type
- single nucleotide variant
- Location
- chr19:11241944 (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-1643-plus-101g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown