DOCK7 p.Pro1109=
c.3327G>A · rs750861708 · VCV777556
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
Conditions
1
developmental and epileptic encephalopathy, 23
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.118 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.39 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 0.5 | GERP -4.3, phastCons 1 |
| Overall | ||
| CADD | 10.54 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/59,972 alleles
Filtering AF
0.00165%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00142%
Overall
0.00211%
34/1,613,542 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 19,991 |
| African / African-American | 0.00267% | 37,445 |
| European (non-Finnish) | 0.00237% | 42,135 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,454 |
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
- DOCK7
- Protein
- p.Pro1109=
- Coding
- c.3327G>A
- MANE Select
- NM_001367561
- dbSNP
- rs750861708
- Type
- single nucleotide variant
- Location
- chr1:62538035 (GRCh38)
- Gene constraint
- LOEUF 0.551 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.60 · 2 PDB
Similar variants
- DOCK7 p.Pro1109Leu Uncertain significance ★★ ⚠ same residue
- DOCK7 c.4924-1G>A Pathogenic/Likely pathogenic ★★ same condition
- DOCK7 p.Arg1380Ter Pathogenic ★★ same condition
- DOCK7 p.Arg1415Ter Pathogenic/Likely pathogenic ★★ same condition
- DOCK7 p.Arg429Ter Pathogenic/Likely pathogenic ★★ same condition
- DOCK7 p.Arg445Ter Pathogenic/Likely pathogenic ★★ same condition
- DOCK7 c.3781+4C>G Uncertain significance ★★ same condition
- DOCK7 c.38+6T>C Uncertain significance ★★ same condition
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/dock7-p-pro1109 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown