DOCK3 p.Ala320=
c.960G>A · rs556907316 · VCV2653862
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0396%, sas)
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 -13 | GERP -4.7 |
| Overall | ||
| CADD | 0.755 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0396%
South Asian · 36/90,906 alleles
Filtering AF
0.0293%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0258%
Overall
0.00372%
60/1,613,112 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0396% | 2,525 |
| Admixed American | 0.01% | 9,985 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,493 |
| African / African-American | 0.00666% | 15,005 |
| European (non-Finnish) | 0.000678% | 147,434 |
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
- DOCK3
- Protein
- p.Ala320=
- Coding
- c.960G>A
- MANE Select
- NM_004947
- dbSNP
- rs556907316
- Type
- single nucleotide variant
- Location
- chr3:51160625 (GRCh38)
- Gene constraint
- LOEUF 0.298 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 75.52
- Residue 320
- a UniProt-annotated variant site (in nedidha)
Similar variants
- DOCK3 p.Arg1609Trp Uncertain significance ★★ ⚠ same type
- DOCK3 p.Arg1787Gln Uncertain significance ★★ ⚠ same type
- DOCK3 p.Arg2020Cys Uncertain significance ★★ ⚠ same type
- DOCK3 p.Arg392Gln Uncertain significance ★★ ⚠ same type
- DOCK3 p.Arg486His Uncertain significance ★★ ⚠ same type
- DOCK3 p.Gly1699Cys Uncertain significance ★★ ⚠ same type
- DOCK3 p.Leu1982Arg Uncertain significance ★★ ⚠ same type
- DOCK3 p.Lys1296Arg 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/dock3-p-ala320 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown