DCDC2 p.Lys39=
c.117G>A · rs1760499891 · VCV994593
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.44 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.6 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 19.53 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- DCDC2
- Protein
- p.Lys39=
- Coding
- c.117G>A
- MANE Select
- NM_016356
- dbSNP
- rs1760499891
- Type
- single nucleotide variant
- Location
- chr6:24357634 (GRCh38)
- Gene constraint
- LOEUF 1.062 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.93 · 1 PDB
- Residue 39
- the doublecortin 1 domain
Similar variants
- DCDC2 c.294-2A>G Pathogenic ★★ same type
- DCDC2 c.349-2A>G Pathogenic ★★ same type
- DCDC2 c.705-2A>G Pathogenic ★★ same type
- DCDC2 p.Leu297Ter Pathogenic ★★ same type
- DCDC2 p.Met1Arg Pathogenic/Likely pathogenic ★★ ⚠ same type
- DCDC2 p.Ser128Ter Pathogenic/Likely pathogenic ★★ same type
- DCDC2 p.Ala153Gly Uncertain significance ★★ ⚠ same type
- DCDC2 p.Ala356Pro 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/dcdc2-p-lys39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown