DOCK11 p.Phe1513=
c.4539T>C · rs764133219 · VCV2661270
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0453%, 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 1.1 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 8.516 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0453%
South Asian · 25/55,225 alleles
Filtering AF
0.0314%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0268%
Overall
0.00889%
107/1,203,224 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0453% | 2,209 |
| European (non-Finnish) | 0.00862% | 11,598 |
| Remaining individualsnot grpmax-eligible | 0.00634% | 15,769 |
| Finnishnot grpmax-eligible | 0.00215% | 46,440 |
| African / African-American | 0.00176% | 56,776 |
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.Phe1513=
- Coding
- c.4539T>C
- MANE Select
- NM_144658
- dbSNP
- rs764133219
- Type
- single nucleotide variant
- Location
- chrX:118649085 (GRCh38)
- Structure
- AlphaFold pLDDT 79.65
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-phe1513 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown