DOCK9 p.Thr744=
c.2232G>C · rs146038138 · VCV2643887
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.798%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.21 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -9.1 | GERP -5 |
| Overall | ||
| CADD | 0.402 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.798%
South Asian · 722/90,494 alleles
Filtering AF
0.75%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.73%
Overall
0.241%
3,889/1,611,524 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.798% | 125 |
| Ashkenazi Jewishnot grpmax-eligible | 0.541% | 185 |
| Middle Eastern | 0.446% | 224 |
| Remaining individualsnot grpmax-eligible | 0.257% | 390 |
| Admixed American | 0.236% | 423 |
| European (non-Finnish) | 0.225% | 445 |
| African / African-American | 0.036% | 2,776 |
| Finnishnot grpmax-eligible | 0.00625% | 15,988 |
| East Asian | 0.00224% | 44,712 |
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.Thr744=
- Coding
- c.2232G>C
- MANE Select
- NM_001366683
- dbSNP
- rs146038138
- Type
- single nucleotide variant
- Location
- chr13:98885736 (GRCh38)
- Gene constraint
- LOEUF 0.425 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 79.68 · 4 PDB
- Residue 744
- the c2 dock-type domain
Similar variants
- DOCK9 p.Ala434Val Benign ★★ same type
- DOCK9 p.Asn1709= 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
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-thr744 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown