Is DSC2 p.Asn413fs (c.1239del) pathogenic?

DSC2 p.Asn413fs (c.1239del) is classified Pathogenic in DSC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-05-01). Absent from gnomAD.

How common is DSC2 p.Asn413fs (c.1239del) in the general population?

DSC2 p.Asn413fs (c.1239del) is absent from gnomAD (gnomAD).

DSC2 p.Asn413fs

c.1239del · rs2144818920 · VCV1694869

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 5.9	GERP 2, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DSC2
Protein: p.Asn413fs
Coding: c.1239del
MANE Select: NM_024422
dbSNP: rs2144818920
Type: Deletion
Location: chr18:31082262 (GRCh38)
Gene constraint: LOEUF 0.743 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 77.26 · 3 PDB
Residue 413: the cadherin 3 domain

Full DSC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DSC2 p.Asn413Ile Uncertain significance ★★ ⚠ same residue
DSC2 p.Asn413Lys Uncertain significance ★★ ⚠ same residue
DSC2 p.Asn413Ser Uncertain significance ★★ ⚠ same residue
DSC2 p.Gln158fs Pathogenic/Likely pathogenic ★★ same type
DSC2 p.Ile26fs Pathogenic/Likely pathogenic ★★ same type
DSC2 p.Leu229fs Pathogenic ★★ same type
DSC2 p.Lys42fs Pathogenic/Likely pathogenic ★★ same type
DSC2 p.Phe708fs Pathogenic/Likely pathogenic ★★ 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-asn413fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown