DCDC2 c.557+1G>T
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
canonical splice-site (±1/±2)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
DCDC2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Consequence | canonical splice-site (±1/±2) | predicted loss-of-function |
|---|---|---|
| Splicing | ||
| Splice region | donor +1 | canonical splice dinucleotide (donor +1) · inside the BP7-excluded zone |
| SpliceAI | Δ0.88 | donor loss · deltas |
| Pangolin | Δ0.84 | loss · gain 0.34 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.6 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 34.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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
- Coding
- c.557+1G>T
- MANE Select
- NM_016356
- dbSNP
- rs763299947
- Type
- single nucleotide variant
- Location
- chr6:24301714 (GRCh38)
- Gene constraint
- LOEUF 1.062 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 63.93 · 1 PDB
Disease context
DCDC2-related disorder
Similar variants
- DCDC2 c.705-2A>G Pathogenic ★★ same condition
- DCDC2 p.Gln448Lys Uncertain significance ★ ⚠ same condition
- DCDC2 p.Gln417Ter Likely pathogenic same condition
- DCDC2 p.Gly368Glu Uncertain significance ⚠ same condition
- DCDC2 p.Lys249Gln Uncertain significance ⚠ same condition
- DCDC2 c.1326+6T>G Likely benign same condition
- DCDC2 c.704+6T>C Likely benign same condition
- DCDC2 c.*10A>G Likely benign same condition
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-c-557-plus-1g-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown