DOCK3 p.Ala1688=
c.5064G>A · rs146000863 · VCV1335527
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.336%, amr)
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>T here scores Δ0.21 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.6 | GERP -5.5 |
| Overall | ||
| CADD | 6.174 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.336%
Admixed American · 201/59,890 alleles
Filtering AF
0.322%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.318%
Overall
0.29%
4,686/1,613,084 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.336% | 298 |
| European (non-Finnish) | 0.33% | 303 |
| South Asian | 0.302% | 331 |
| Ashkenazi Jewishnot grpmax-eligible | 0.287% | 348 |
| Remaining individualsnot grpmax-eligible | 0.274% | 365 |
| Middle Eastern | 0.115% | 866 |
| Amishnot grpmax-eligible | 0.11% | 910 |
| African / African-American | 0.0533% | 1,875 |
| Finnishnot grpmax-eligible | 0.0109% | 9,138 |
| East Asian | 0.00446% | 22,420 |
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
- DOCK3
- Protein
- p.Ala1688=
- Coding
- c.5064G>A
- MANE Select
- NM_004947
- dbSNP
- rs146000863
- Type
- single nucleotide variant
- Location
- chr3:51361916 (GRCh38)
- Gene constraint
- LOEUF 0.298 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 75.52
- Residue 1688
- a UniProt-annotated variant site (in nedidha)
Similar variants
- DOCK3 p.Arg1609Trp Uncertain significance ★★ ⚠ same type
- DOCK3 p.Arg1787Gln Uncertain significance ★★ ⚠ same type
- DOCK3 p.Arg2020Cys Uncertain significance ★★ ⚠ same type
- DOCK3 p.Arg392Gln Uncertain significance ★★ ⚠ same type
- DOCK3 p.Arg486His Uncertain significance ★★ ⚠ same type
- DOCK3 p.Gly1699Cys Uncertain significance ★★ ⚠ same type
- DOCK3 p.Leu1982Arg Uncertain significance ★★ ⚠ same type
- DOCK3 p.Lys1296Arg Uncertain significance ★★ ⚠ 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/dock3-p-ala1688 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown