DOK7 p.Ser533=
c.1599G>A · rs115742102 · VCV1206514
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.16%, afr)
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 -5.3 | GERP -1.7 |
| Overall | ||
| CADD | 1.113 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.16%
African / African-American · 848/73,110 alleles
Filtering AF
1.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.07%
Overall
0.0636%
977/1,535,886 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.16% | 86 |
| Remaining individualsnot grpmax-eligible | 0.0883% | 1,132 |
| Admixed American | 0.0824% | 1,214 |
| Middle Eastern | 0.0167% | 5,990 |
| South Asian | 0.00714% | 14,010 |
| East Asian | 0.00245% | 40,890 |
| European (non-Finnish) | 0.00227% | 44,107 |
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
- DOK7
- Protein
- p.Ser533=
- Coding
- c.1599G>A
- MANE Select
- NM_173660 · reported on NM_001301071
- dbSNP
- rs115742102
- Type
- single nucleotide variant
- Location
- chr4:3500309 (GRCh38)
- Gene constraint
- LOEUF 1.658 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 65.61
Similar variants
- DOK7 c.331+1G>T Pathogenic ★★ same type
- DOK7 c.332-1G>A Likely pathogenic ★★ same type
- DOK7 c.332-1G>C Likely pathogenic ★★ same type
- DOK7 c.332-1G>T Likely pathogenic ★★ same type
- DOK7 p.Arg158Gln Pathogenic/Likely pathogenic ★★ same type
- DOK7 p.Arg201Ter Pathogenic ★★ same type
- DOK7 p.Cys412Ter Pathogenic ★★ same type
- DOK7 p.Gln151Ter Pathogenic/Likely pathogenic ★★ 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/dok7-p-ser533 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown