DOCK7 p.Lys1104=
c.3312G>A · rs1002333745 · VCV1626737
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Conditions
1
developmental and epileptic encephalopathy, 23
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.304 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.25 | acceptor gain · deltas |
| Constraint at this position | ||
| Conservation | phyloP 3.3 | GERP -0.59, phastCons 1 |
| Overall | ||
| CADD | 14.86 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/59,974 alleles
Overall
6.2e-05%
1/1,613,546 alleles · very rare
exomes 1/1,461,292 · genomes 0/152,254 · joint denominator
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.Lys1104=
- Coding
- c.3312G>A
- MANE Select
- NM_001367561
- dbSNP
- rs1002333745
- Type
- single nucleotide variant
- Location
- chr1:62538050 (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 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
- DOCK7 p.Ala1479Thr 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-lys1104 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown