DOCK6 p.Glu463=
c.1389G>A · rs59220455 · VCV754598
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.577%, afr)
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 0.28 | GERP -4.7, phastCons 0.99 |
| Overall | ||
| CADD | 8.227 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.577%
African / African-American · 433/75,054 alleles
Filtering AF
0.532%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.514%
Overall
0.0318%
513/1,613,794 alleles · rare
exomes 282/1,461,440 · genomes 231/152,354 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.577% | 173 |
| Admixed American | 0.03% | 3,335 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,206 |
| European (non-Finnish) | 0.00424% | 23,594 |
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.Glu463=
- Coding
- c.1389G>A
- MANE Select
- NM_020812
- dbSNP
- rs59220455
- Type
- single nucleotide variant
- Location
- chr19:11243150 (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-p-glu463 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown