DOCK4 p.Lys472=
c.1416A>G · rs116208701 · VCV785230
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.724%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.215 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.45 | GERP -3.8, phastCons 0.14 |
| Overall | ||
| CADD | 5.371 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.724%
African / African-American · 543/75,028 alleles
Filtering AF
0.673%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.653%
Overall
0.0413%
666/1,613,436 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.724% | 138 |
| Middle Eastern | 0.412% | 242 |
| Remaining individualsnot grpmax-eligible | 0.0768% | 1,302 |
| Admixed American | 0.0233% | 4,284 |
| South Asian | 0.0033% | 30,279 |
| European (non-Finnish) | 0.0028% | 35,749 |
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.Lys472=
- Coding
- c.1416A>G
- MANE Select
- NM_001363540
- dbSNP
- rs116208701
- Type
- single nucleotide variant
- Location
- chr7:111900438 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.47
- Residue 472
- the c2 dock-type domain
Similar variants
- 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
- DOCK4 p.Arg106His 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-lys472 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown