DOCK3 p.Asp676=
c.2028C>T · rs200554524 · VCV3053419
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.299%, afr)
Conditions
1
DOCK3-related disorder
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 1.1 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 9.372 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.299%
African / African-American · 224/75,008 alleles
Filtering AF
0.267%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.254%
Overall
0.0156%
252/1,613,316 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.299% | 335 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.0134% | 7,485 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,494 |
| South Asian | 0.00441% | 22,701 |
| European (non-Finnish) | 0.000848% | 117,972 |
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.Asp676=
- Coding
- c.2028C>T
- MANE Select
- NM_004947
- dbSNP
- rs200554524
- Type
- single nucleotide variant
- Location
- chr3:51237516 (GRCh38)
- Gene constraint
- LOEUF 0.298 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 75.52
- Residue 676
- a UniProt-annotated variant site (in nedidha)
Disease context
DOCK3-related disorder
Similar variants
- DOCK3 c.1037+1G>A Likely pathogenic ★ same condition
- DOCK3 p.Arg362Ter Likely pathogenic ★ same condition
- DOCK3 c.2548+6T>A Benign same condition
- DOCK3 c.3915+10A>G Likely benign same condition
- DOCK3 c.5412+10C>T Likely benign same condition
- DOCK3 p.Asp1841= Likely benign same condition
- DOCK3 p.Leu99= Likely benign same condition
- DOCK3 p.Pro1852= Likely benign same condition
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-asp676 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown