rs1555637555

Variant names:

• chr18-31071613-AATGCT-A
• rs1555637555
• NM_024422.6:c.2112_2116delAGCAT

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_024422.6(DSC2):​c.2112_2116delAGCAT​(p.Phe708HisfsTer14) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DSC2 NM_024422.6 frameshift
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:2
• Conservation: PhyloP100: 4.34

Genes affected

DSC2 (HGNC:3036): (desmocollin 2) This gene encodes a member of the desmocollin protein subfamily. Desmocollins, along with desmogleins, are cadherin-like transmembrane glycoproteins that are major components of the desmosome. Desmosomes are cell-cell junctions that help resist shearing forces and are found in high concentrations in cells subject to mechanical stress. This gene is found in a cluster with other desmocollin family members on chromosome 18. Mutations in this gene are associated with arrhythmogenic right ventricular dysplasia-11, and reduced protein expression has been described in several types of cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 18-31071613-AATGCT-A is Pathogenic according to our data. Variant chr18-31071613-AATGCT-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 523695.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DSC2	NM_024422.6	c.2112_2116delAGCAT	p.Phe708HisfsTer14	frameshift_variant	Exon 13 of 16	ENST00000280904.11	NP_077740.1
DSC2	NM_004949.5	c.2112_2116delAGCAT	p.Phe708HisfsTer14	frameshift_variant	Exon 13 of 17		NP_004940.1
DSC2	NM_001406506.1	c.1683_1687delAGCAT	p.Phe565HisfsTer14	frameshift_variant	Exon 13 of 16		NP_001393435.1
DSC2	NM_001406507.1	c.1683_1687delAGCAT	p.Phe565HisfsTer14	frameshift_variant	Exon 13 of 17		NP_001393436.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSC2	ENST00000280904.11	c.2112_2116delAGCAT	p.Phe708HisfsTer14	frameshift_variant	Exon 13 of 16	1	NM_024422.6	ENSP00000280904.6
DSC2	ENST00000251081.8	c.2112_2116delAGCAT	p.Phe708HisfsTer14	frameshift_variant	Exon 13 of 17	1		ENSP00000251081.6
DSC2	ENST00000648081.1	c.1683_1687delAGCAT	p.Phe565HisfsTer14	frameshift_variant	Exon 14 of 17			ENSP00000497441.1
DSC2	ENST00000682357.1	c.1683_1687delAGCAT	p.Phe565HisfsTer14	frameshift_variant	Exon 13 of 16			ENSP00000507826.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Arrhythmogenic right ventricular dysplasia 11 Pathogenic:1

Jul 11, 2022

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Phe708Hisfs*14) in the DSC2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DSC2 are known to be pathogenic (PMID: 23911551). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with arrhythmogenic cardiomyopathy (PMID: 33258288). ClinVar contains an entry for this variant (Variation ID: 523695). For these reasons, this variant has been classified as Pathogenic. -

not provided Pathogenic:1

Apr 10, 2017

Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1555637555; hg19: chr18-28651579;