Is DSC2 p.Glu102Lys (c.304G>A) pathogenic?

DSC2 p.Glu102Lys (c.304G>A) is classified Conflicting classifications of pathogenicity in DSC2 (ClinVar, Conflicting submitters, 20 submitters; last evaluated 2026-06-01). AlphaMissense: likely benign (0.073); Rare (popmax 0.148%, nfe); Associated with Cardiovascular phenotype.

What condition is associated with DSC2 p.Glu102Lys (c.304G>A)?

DSC2 p.Glu102Lys (c.304G>A) is associated with Cardiovascular phenotype, cardiomyopathy, arrhythmogenic right ventricular dysplasia 11 (ClinVar).

How common is DSC2 p.Glu102Lys (c.304G>A) in the general population?

DSC2 p.Glu102Lys (c.304G>A) is rare (popmax 0.148%, nfe) (gnomAD).

What do computational predictors say about DSC2 p.Glu102Lys (c.304G>A)?

AlphaMissense predicts likely benign (score 0.073) — an in-silico prediction, not a clinical call.

DSC2 p.Glu102Lys

c.304G>A · rs144799937 · VCV46189

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 20 submitters

AlphaMissense

likely benign

0.073 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.148%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.073	likely benign
REVEL	0.277	benign-leaning
SaProt	LLR -5.95	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.2	GERP 0.065, phastCons 0.48
Regional constraint	o/e 0.98	unconstrained · MANE · 34 kb · p 0.48 · regional, not allelic
Overall
CADD	17.82	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.148% European (non-Finnish) · 1,749/1,179,532 alleles

Filtering AF 0.142% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.14%

Overall 0.123% 1,981/1,613,078 alleles · rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.22%	455
European (non-Finnish)grpmax	0.148%	674
Remaining individualsnot grpmax-eligible	0.123%	811
Middle Eastern	0.0661%	1,513
South Asian	0.0571%	1,750
Finnishnot grpmax-eligible	0.025%	3,999
Admixed American	0.02%	4,996
African / African-American	0.00802%	12,470

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DSC2
Protein: p.Glu102Lys
Coding: c.304G>A
MANE Select: NM_024422
dbSNP: rs144799937
Type: single nucleotide variant
Location: chr18:31092151 (GRCh38)
Gene constraint: LOEUF 0.743 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 77.26 · 3 PDB
Residue 102: a UniProt-annotated variant site (in arvd11; uncertain significance; abolishes localization at desmosomes and partially mis-localizes to the cytoplasm; uncertain significance)

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

Disease context

Cardiovascular phenotype — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: cardiomyopathy arrhythmogenic right ventricular dysplasia 11 familial isolated arrhythmogenic right ventricular dysplasia arrhythmogenic right ventricular cardiomyopathy

Similar variants

DSC2 p.Glu102Asp Uncertain significance ★ ⚠ same residue
DSC2 p.Glu102= Likely benign ★ same residue
DSC3 p.Arg102Lys Benign ★★ same residue
DSC2 c.1521-1G>A Likely pathogenic ★★ same condition
DSC2 c.1664-1G>A Likely pathogenic ★★ same condition
DSC2 c.354+2T>A Likely pathogenic ★★ same condition
DSC2 c.355-1G>A Likely pathogenic ★★ same condition
DSC2 p.Gln554Ter Pathogenic ★★ 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/dsc2-p-glu102lys (accessed [today's date]).

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