Is DSC2 p.His849Pro (c.2546A>C) pathogenic?

DSC2 p.His849Pro (c.2546A>C) is classified Likely benign in DSC2 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-11-12). AlphaMissense: likely benign (0.0731); Rare (popmax 0.112%, amr); Associated with Cardiovascular phenotype.

What condition is associated with DSC2 p.His849Pro (c.2546A>C)?

DSC2 p.His849Pro (c.2546A>C) is associated with Cardiovascular phenotype, cardiomyopathy, arrhythmogenic right ventricular dysplasia 11 (ClinVar).

How common is DSC2 p.His849Pro (c.2546A>C) in the general population?

DSC2 p.His849Pro (c.2546A>C) is rare (popmax 0.112%, amr) (gnomAD).

What do computational predictors say about DSC2 p.His849Pro (c.2546A>C)?

AlphaMissense predicts likely benign (score 0.0731) — an in-silico prediction, not a clinical call.

DSC2 p.His849Pro

c.2546A>C · rs184487763 · VCV926569

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.0731 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.112%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Cardiovascular phenotype

Computational evidence

Protein change
AlphaMissense	0.0731	likely benign
REVEL	0.093	moderately benign-leaning
SaProt	LLR -5.97	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 -3.1, phastCons 0.83
Regional constraint	o/e 0.98	unconstrained · MANE · 34 kb · p 0.48 · regional, not allelic
Overall
CADD	13.21	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 0.112% Admixed American · 67/60,028 alleles

Filtering AF 0.0901% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0823%

Overall 0.0044% 71/1,614,152 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.112%	896
Remaining individualsnot grpmax-eligible	0.0032%	31,252
African / African-American	0.00133%	75,058
South Asian	0.0011%	91,080

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.His849Pro
Coding: c.2546A>C
MANE Select: NM_024422
dbSNP: rs184487763
Type: single nucleotide variant
Location: chr18:31068175 (GRCh38)
Gene constraint: LOEUF 0.743 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 77.26 · 3 PDB
Residue 849: a UniProt-annotated variant site (in arvd11; likely pathogenic; mislocalization of dsc2 to the cytoplasm within intercalated disks of the heart)

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

Similar variants

DSC2 p.His849Tyr Uncertain significance ★★ ⚠ same residue
DSC2 p.His849Arg Uncertain significance ★ ⚠ same residue
DSC2 p.His849= Likely 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-his849pro (accessed [today's date]).

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