DOCK6 p.Pro653=
c.1959C>T · rs200269584 · VCV785608
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.87%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.80 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.7 | GERP -5.3 |
| Overall | ||
| CADD | 4.043 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.87%
African / African-American · 651/74,808 alleles
Filtering AF
0.815%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.793%
Overall
0.0498%
796/1,597,574 alleles · rare
exomes 411/1,445,422 · genomes 385/152,152 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.87% | 115 |
| Middle Eastern | 0.133% | 751 |
| Remaining individualsnot grpmax-eligible | 0.0646% | 1,547 |
| Admixed American | 0.049% | 2,042 |
| European (non-Finnish) | 0.00563% | 17,769 |
| South Asian | 0.00339% | 29,455 |
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.Pro653=
- Coding
- c.1959C>T
- MANE Select
- NM_020812
- dbSNP
- rs200269584
- Type
- single nucleotide variant
- Location
- chr19:11237653 (GRCh38)
- Gene constraint
- LOEUF 0.87 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.78 · 7 PDB
- Residue 653
- the c2 dock-type domain
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-p-pro653 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown