DYRK2 p.Pro11=
c.33C>T · rs200090077 · VCV790666
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.23%, afr)
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 0.3 | GERP 0.45, phastCons 0.99 |
| Overall | ||
| CADD | 13.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.23%
African / African-American · 852/69,272 alleles
Filtering AF
1.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.13%
Overall
0.0642%
972/1,513,424 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.23% | 81 |
| Remaining individualsnot grpmax-eligible | 0.0741% | 1,350 |
| Admixed American | 0.0707% | 1,415 |
| Middle Eastern | 0.0177% | 5,654 |
| European (non-Finnish) | 0.00364% | 27,482 |
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
- DYRK2
- Protein
- p.Pro11=
- Coding
- c.33C>T
- MANE Select
- NM_006482
- dbSNP
- rs200090077
- Type
- single nucleotide variant
- Location
- chr12:67649166 (GRCh38)
- Gene constraint
- LOEUF 0.494 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 77.04 · 26 PDB
- Residue 11
- the 'disordered' region
Similar variants
- DYRK2 p.Ala413Gly Uncertain significance ★ ⚠ same type
- DYRK2 p.Ala499Thr Uncertain significance ★ ⚠ same type
- DYRK2 p.Ala499Val Uncertain significance ★ ⚠ same type
- DYRK2 p.Ala581Val Uncertain significance ★ ⚠ same type
- DYRK2 p.Ala9Val Uncertain significance ★ ⚠ same type
- DYRK2 p.Arg125Gln Uncertain significance ★ ⚠ same type
- DYRK2 p.Arg268Gln Uncertain significance ★ ⚠ same type
- DYRK2 p.Arg274Trp 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/dyrk2-p-pro11 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown