DSC2 p.Thr412fs
c.1234dup · rs397517390 · VCV46164
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
ultra-rare (gnomAD MAF 1.428e-06)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 9 of 16 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 7.4 | GERP 2, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
dbSNP / gnomAD
Global frequency
0.000143%
via dbSNP · ultra-rare
No ancestry breakdown or filtering allele frequency is available for this variant, so BA1/BS1 cannot be assessed from this figure alone.
Variant & gene context
- Gene
- DSC2
- Protein
- p.Thr412fs
- Coding
- c.1234dup
- MANE Select
- NM_024422 · reported on NM_004949
- dbSNP
- rs397517390
- Type
- Duplication
- Location
- chr18:31082266 (GRCh38)
- Gene constraint
- LOEUF 0.743 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.26 · 3 PDB
- Residue 412
- a turn; the cadherin 3 domain
Similar variants
- DSC2 p.Leu396fs Pathogenic ★★ same type
- DSC2 p.Gly12_Ala13insGly Uncertain significance ★★ same type
- DSC2 c.2126-15dup Likely benign ★★ same type
- DSC2 c.631-13dup Benign/Likely benign ★★ same type
- DSC2 c.70-18dup Benign/Likely benign ★★ same type
- DSC2 c.70-8dup Benign/Likely benign ★★ same type
- DSC2 c.942+13_942+15dup Benign/Likely benign ★★ same type
- DSC2 c.943-9dup Benign/Likely benign ★★ 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/dsc2-p-thr412fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown