DOCK7 p.Phe1174=
c.3522T>C · rs753000635 · VCV475139
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00833%, 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. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP -2, phastCons 0.99 |
| Overall | ||
| CADD | 8.063 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00833%
Admixed American · 5/60,006 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.000743%
12/1,614,056 alleles · very rare
exomes 7/1,461,688 · genomes 5/152,368 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00833% | 12,001 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,501 |
| African / African-American | 0.00266% | 37,537 |
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.Phe1174=
- Coding
- c.3522T>C
- MANE Select
- NM_001367561
- dbSNP
- rs753000635
- Type
- single nucleotide variant
- Location
- chr1:62535582 (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.Phe1174Cys 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-phe1174 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown