DOCK9 p.Asn1709=
c.5127C>T · rs11617965 · VCV781704
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.943%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.253 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -6.3 | GERP -4.9 |
| Overall | ||
| CADD | 3.62 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.943%
Middle Eastern · 57/6,044 alleles
Filtering AF
0.747%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.677%
Overall
0.274%
4,419/1,613,662 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.943% | 106 |
| Ashkenazi Jewishnot grpmax-eligible | 0.919% | 109 |
| Remaining individualsnot grpmax-eligible | 0.386% | 259 |
| European (non-Finnish) | 0.279% | 358 |
| Finnishnot grpmax-eligible | 0.234% | 427 |
| South Asian | 0.227% | 440 |
| Admixed American | 0.217% | 462 |
| African / African-American | 0.0893% | 1,120 |
| East Asian | 0.00446% | 22,441 |
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
- DOCK9
- Protein
- p.Asn1709=
- Coding
- c.5127C>T
- MANE Select
- NM_001366683
- dbSNP
- rs11617965
- Type
- single nucleotide variant
- Location
- chr13:98824401 (GRCh38)
- Gene constraint
- LOEUF 0.425 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.68 · 4 PDB
- Residue 1709
- the docker domain; a β-strand; the 'interaction with cdc42' region
Similar variants
- DOCK9 p.Ala434Val Benign ★★ same type
- DOCK9 p.Cys2012= Benign/Likely benign ★★ same type
- DOCK9 p.Leu1435= Benign ★★ same type
- DOCK9 c.5023+908C>T Uncertain significance ★ ⚠ same type
- DOCK9 c.5023+919C>T Uncertain significance ★ ⚠ same type
- DOCK9 c.5023+952C>T Uncertain significance ★ ⚠ same type
- DOCK9 c.5367+706T>A Uncertain significance ★ ⚠ same type
- DOCK9 p.Ala100Ser Uncertain significance ★ ⚠ 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/dock9-p-asn1709 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown