DOCK7 p.Lys130=
c.390A>G · rs550800563 · VCV1055982
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0285%, amr)
Conditions
2
Inborn genetic diseases
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 -0.28 | GERP -5, phastCons 0.35 |
| Overall | ||
| CADD | 5.716 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0285%
Admixed American · 9/31,584 alleles
Filtering AF
0.0148%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.011%
Overall
0.0024%
31/1,290,348 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0285% | 3,509 |
| Remaining individualsnot grpmax-eligible | 0.0041% | 24,367 |
| East Asian | 0.00285% | 35,042 |
| European (non-Finnish) | 0.00195% | 51,375 |
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.Lys130=
- Coding
- c.390A>G
- MANE Select
- NM_001367561
- dbSNP
- rs550800563
- Type
- single nucleotide variant
- Location
- chr1:62648544 (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.Lys130Asn 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-lys130 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown