DCC c.3898+2T>C
Likely pathogenic
Single submitter
Classification
Likely 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
DCC-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 in a LoF-intolerant gene |
|---|---|---|
| Splicing | ||
| Splice region | donor +2 | canonical splice dinucleotide (donor +2) · inside the BP7-excluded zone |
| SpliceAI | Δ0.86 | donor loss · deltas |
| Pangolin | Δ0.45 | loss · gain 0.10 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.32 | GERP 1.9, phastCons 0.98 |
| Non-coding constraint | Z -1.12 | 1 kb window · o/e 1.08 · regional · uncalibrated |
| Overall | ||
| CADD | 21.6 | 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
- DCC
- Coding
- c.3898+2T>C
- MANE Select
- NM_005215
- Type
- single nucleotide variant
- Location
- chr18:53486960 (GRCh38)
- Gene constraint
- LOEUF 0.414 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 68.60 · 9 PDB
Disease context
DCC-related disorder
Similar variants
- DCC c.2828-1G>A Likely pathogenic ★ same condition
- DCC p.Arg501Ter Likely pathogenic ★ same condition
- DCC p.Glu512Ter Likely pathogenic ★ same condition
- DCC p.Trp508Ter Likely pathogenic ★ same condition
- DCC p.Trp745Ter Likely pathogenic ★ same condition
- DCC p.Pro1086Leu Uncertain significance ⚠ same condition
- DCC p.Thr614Ile Uncertain significance ⚠ same condition
- DCC c.2360-4C>T 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/dcc-c-3898-plus-2t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown