DOCK11 p.Tyr652=
c.1956C>T · rs557084723 · VCV2661267
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0476%, mid)
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 -7.4 | GERP -5.5 |
| Overall | ||
| CADD | 0.258 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0476%
Middle Eastern · 2/4,202 alleles
Filtering AF
0.00839%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0035%
Overall
0.0034%
40/1,174,864 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0476% | 2,101 |
| Remaining individualsnot grpmax-eligible | 0.00651% | 15,349 |
| African / African-American | 0.00536% | 18,642 |
| European (non-Finnish) | 0.00352% | 28,370 |
| Admixed American | 0.00254% | 39,394 |
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
- DOCK11
- Protein
- p.Tyr652=
- Coding
- c.1956C>T
- MANE Select
- NM_144658
- dbSNP
- rs557084723
- Type
- single nucleotide variant
- Location
- chrX:118588297 (GRCh38)
- Structure
- AlphaFold pLDDT 79.65
- Residue 652
- the c2 dock-type domain
Similar variants
- DOCK11 p.Ala1222Val Uncertain significance ★★ ⚠ same type
- DOCK11 p.Ala1665Val Uncertain significance ★★ ⚠ same type
- DOCK11 p.Leu781His Uncertain significance ★★ ⚠ same type
- DOCK11 p.Gln866Arg Benign ★★ same type
- DOCK11 p.Ser842Leu Likely benign ★★ same type
- DOCK11 c.1718+5G>A Pathogenic ★ same type
- DOCK11 c.392+1G>A Likely pathogenic ★ same type
- DOCK11 c.4582-1G>A 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/dock11-p-tyr652 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown