DOCK3 p.Glu1708=
c.5124G>A · rs184200474 · VCV1711576
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.162%, nfe)
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 5.6 | GERP -0.44, phastCons 1 |
| Overall | ||
| CADD | 8.096 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.162%
European (non-Finnish) · 1,910/1,177,960 alleles
Filtering AF
0.156%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.154%
Overall
0.126%
2,030/1,609,516 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.162% | 617 |
| Remaining individualsnot grpmax-eligible | 0.0962% | 1,039 |
| Admixed American | 0.0404% | 2,476 |
| Finnishnot grpmax-eligible | 0.0282% | 3,542 |
| African / African-American | 0.024% | 4,165 |
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.Glu1708=
- Coding
- c.5124G>A
- MANE Select
- NM_004947
- dbSNP
- rs184200474
- Type
- single nucleotide variant
- Location
- chr3:51361976 (GRCh38)
- Gene constraint
- LOEUF 0.298 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 75.52
- Residue 1708
- 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-glu1708 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown