DOCK3 p.Val1357=
c.4071C>T · VCV4962776
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
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 · C>A here scores Δ0.70 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -12 | GERP -5.9 |
| Overall | ||
| CADD | 0.358 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,060 alleles
Filtering AF
0.00402%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00362%
Overall
0.0044%
71/1,612,414 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,060 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,604 |
| African / African-American | 0.00534% | 18,717 |
| European (non-Finnish) | 0.00509% | 19,659 |
| East Asian | 0.00223% | 44,850 |
| South Asian | 0.0011% | 90,630 |
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.Val1357=
- Coding
- c.4071C>T
- MANE Select
- NM_004947
- Type
- single nucleotide variant
- Location
- chr3:51350356 (GRCh38)
- Gene constraint
- LOEUF 0.298 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 75.52
- Residue 1357
- a UniProt-annotated variant site (in nedidha); the docker domain
Similar variants
- DOCK3 p.Val1357Ile Uncertain significance ★ ⚠ same residue
- 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
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-val1357 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown