DOCK4 p.Thr20=
c.60C>T · VCV3905115
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.367%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.077 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.1 | GERP -4 |
| Overall | ||
| CADD | 3.431 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.367%
African / African-American · 274/74,738 alleles
Filtering AF
0.331%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.317%
Overall
0.0219%
350/1,596,858 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.367% | 273 |
| Remaining individualsnot grpmax-eligible | 0.0371% | 2,694 |
| Admixed American | 0.0363% | 2,754 |
| Middle Eastern | 0.0331% | 3,021 |
| East Asian | 0.0203% | 4,919 |
| European (non-Finnish) | 0.00179% | 55,773 |
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
- DOCK4
- Protein
- p.Thr20=
- Coding
- c.60C>T
- MANE Select
- NM_001363540
- Type
- single nucleotide variant
- Location
- chr7:112004109 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.47
- Residue 20
- the sh3 domain
Similar variants
- DOCK4 p.Thr20Asn Uncertain significance ★ ⚠ same residue
- DOCK4 p.Arg490Trp Uncertain significance ★★ ⚠ same type
- DOCK4 p.Gln1223Arg Uncertain significance ★★ ⚠ same type
- DOCK4 p.His1716Tyr Uncertain significance ★★ ⚠ same type
- DOCK4 p.Pro1641Leu Uncertain significance ★★ ⚠ same type
- DOCK4 p.Ser750Arg Uncertain significance ★★ ⚠ same type
- DOCK4 c.550-8T>C Benign/Likely benign ★★ same type
- DOCK4 p.Arg106Cys Benign/Likely benign ★★ ⚠ 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/dock4-p-thr20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown