DOCK4 p.Ile875=
c.2625A>T · VCV3905524
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0659%, mid)
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 -0.66 | GERP -2.6, phastCons 0.028 |
| Overall | ||
| CADD | 5.613 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0659%
Middle Eastern · 4/6,068 alleles
Filtering AF
0.0472%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0423%
Overall
0.00335%
54/1,612,804 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0659% | 1,517 |
| African / African-American | 0.0614% | 1,627 |
| Admixed American | 0.00334% | 29,934 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,414 |
| European (non-Finnish) | 8.48e-05% | 1,179,422 |
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.Ile875=
- Coding
- c.2625A>T
- MANE Select
- NM_001363540
- Type
- single nucleotide variant
- Location
- chr7:111844874 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 76.47
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-ile875 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown