DOCK3 p.Pro1852=
c.5556A>C · rs782401751 · VCV3057444
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0475%, eas)
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 -3.4 | GERP -4.4 |
| Overall | ||
| CADD | 1.423 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0475%
East Asian · 18/37,896 alleles
Filtering AF
0.0306%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0253%
Overall
0.021%
252/1,198,498 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0475% | 2,105 |
| European (non-Finnish) | 0.0263% | 3,798 |
| Remaining individualsnot grpmax-eligible | 0.017% | 5,881 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00785% | 12,742 |
| African / African-American | 0.00605% | 16,533 |
| South Asian | 0.00484% | 20,647 |
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.Pro1852=
- Coding
- c.5556A>C
- MANE Select
- NM_004947
- dbSNP
- rs782401751
- Type
- single nucleotide variant
- Location
- chr3:51380180 (GRCh38)
- Gene constraint
- LOEUF 0.298 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 75.52
- Residue 1852
- a UniProt-annotated variant site (in nedidha); the 'disordered' region
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.Asp676= Likely benign same condition
- DOCK3 p.Leu99= 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-pro1852 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown