DCLK2 p.Pro21=
c.63G>C · rs368575203 · VCV2655120
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1%, 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 -3.3 | GERP -3.8 |
| Overall | ||
| CADD | 4.044 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1%
African / African-American · 732/73,190 alleles
Filtering AF
0.94%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.916%
Overall
0.0528%
825/1,563,964 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1% | 100 |
| Admixed American | 0.0728% | 1,374 |
| Remaining individualsnot grpmax-eligible | 0.0665% | 1,504 |
| Middle Eastern | 0.0346% | 2,891 |
| South Asian | 0.00122% | 81,966 |
| European (non-Finnish) | 0.00104% | 96,542 |
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
- DCLK2
- Protein
- p.Pro21=
- Coding
- c.63G>C
- MANE Select
- NM_001040260
- dbSNP
- rs368575203
- Type
- single nucleotide variant
- Location
- chr4:150079090 (GRCh38)
- Gene constraint
- LOEUF 0.525 · pLI 0.84 (gnomAD)
- Structure
- AlphaFold pLDDT 70.37
- Residue 21
- the 'disordered' region
Similar variants
- DCLK2 c.961+930C>T Uncertain significance ★ same type
- DCLK2 c.961+955A>G Uncertain significance ★ same type
- DCLK2 c.961+963G>A Uncertain significance ★ same type
- DCLK2 p.Ala176Val Uncertain significance ★ ⚠ same type
- DCLK2 p.Ala178Val Uncertain significance ★ ⚠ same type
- DCLK2 p.Ala27Gly Uncertain significance ★ ⚠ same type
- DCLK2 p.Ala421Ser Uncertain significance ★ ⚠ same type
- DCLK2 p.Ala49Glu 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/dclk2-p-pro21 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown