rs730880092

Variant names:

• chr6-7583571-GA-G
• rs730880092
• NM_004415.4:c.6310delA

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_Strong PP5_Very_Strong

The NM_004415.4(DSP):​c.6310delA​(p.Thr2104GlnfsTer12) variant causes a frameshift change. The variant allele was found at a frequency of 0.0000198 in 1,614,072 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency:
  • Genomes: 𝑓 0.000026 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000019 (0 hom.)
• Consequence: DSP NM_004415.4 frameshift
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:6
• Conservation: PhyloP100: 3.59

Genes affected

DSP (HGNC:3052): (desmoplakin) This gene encodes a protein that anchors intermediate filaments to desmosomal plaques and forms an obligate component of functional desmosomes. Mutations in this gene are the cause of several cardiomyopathies and keratodermas, including skin fragility-woolly hair syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 16 pathogenic variants in the truncated region.
• PP5: Variant 6-7583571-GA-G is Pathogenic according to our data. Variant chr6-7583571-GA-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 180343.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
DSP	NM_004415.4	c.6310delA	p.Thr2104GlnfsTer12	frameshift_variant	Exon 24 of 24	ENST00000379802.8	NP_004406.2
DSP	NM_001319034.2	c.4981delA	p.Thr1661GlnfsTer12	frameshift_variant	Exon 24 of 24		NP_001305963.1
DSP	NM_001008844.3	c.4513delA	p.Thr1505GlnfsTer12	frameshift_variant	Exon 24 of 24		NP_001008844.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DSP	ENST00000379802.8	c.6310delA	p.Thr2104GlnfsTer12	frameshift_variant	Exon 24 of 24	1	NM_004415.4	ENSP00000369129.3
DSP	ENST00000418664.2	c.4513delA	p.Thr1505GlnfsTer12	frameshift_variant	Exon 24 of 24	1		ENSP00000396591.2
DSP	ENST00000710359.1	c.4981delA	p.Thr1661GlnfsTer12	frameshift_variant	Exon 24 of 24			ENSP00000518230.1

Frequencies

GnomAD3 genomes AF: 0.0000263 AC: 4 AN: 152182 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000377

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000517 AC: 13 AN: 251432 Hom.: 0 AF XY: 0.0000442 AC XY: 6 AN XY: 135894

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.000508

Gnomad NFE exome AF: 0.0000176

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000192 AC: 28 AN: 1461890 Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13 AN XY: 727246

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.000468

Gnomad4 NFE exome AF: 0.00000270

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0000263 AC: 4 AN: 152182 Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4 AN XY: 74348

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000377

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Cardiomyopathy Pathogenic:2

Jan 08, 2015

Blueprint Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dec 16, 2020

Color Diagnostics, LLC DBA Color Health

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant deletes 1 nucleotide in exon 24 of the DSP gene, creating a frameshift and premature translation stop signal in the last exon. This variant is expected to result in the expression of a truncated protein product lacking C-terminal plakin repeat domains that bind intermediate filaments. This variant has been reported in heterozygous state in ten unrelated Finnish individuals (PMID: 26084686, 32005173), including nine individuals affected with dilated cardiomyopathy and one affected individual with slightly dilated ventricles. Subsequently, seven additional family members have been identified to carry this variant. Four of these individuals were affected with dilated cardiomyopathy or other cardiac abnormalities, and three individuals were unaffected. Furthermore, most of the carriers with dilated cardiomyopathy showed an arrhythmogenic phenotype (PMID: 32005173). This variant has also been reported in the compound heterozygous state with another truncation or missense variant in two individuals affected with severe cardiomyopathies and skin, hair, and/or tooth abnormalities (PMID: 19924139, 24341478). Desmoplakin was either not expressed or reduced in skin biopsies from the two individuals. Heterozygous family members were unaffected in both families. This variant has been identified in 13/251432 chromosomes (11/21648 Finnish European chromosomes) in the general population by the Genome Aggregation Database (gnomAD). Multiple truncations variants that lie downstream of this variant are known to cause arrhythmogenic right ventricular cardiomyopathy and dilated cardiomyopathy (ClinVar). Loss of DSP function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Likely Pathogenic. -

Arrhythmogenic cardiomyopathy with wooly hair and keratoderma Pathogenic:1

Jun 12, 2023

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Arrhythmogenic right ventricular dysplasia 8;C1854063:Arrhythmogenic cardiomyopathy with wooly hair and keratoderma Pathogenic:1

Feb 21, 2024

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.Thr2104Glnfs*12) in the DSP gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 768 amino acid(s) of the DSP protein. This variant is present in population databases (rs730880092, gnomAD 0.05%). This premature translational stop signal has been observed in individual(s) with clinical features of DSP-related conditions (PMID: 19924139, 24341478, 35653365). ClinVar contains an entry for this variant (Variation ID: 180343). This variant disrupts a region of the DSP protein in which other variant(s) (p.Glu2728Glyfs*11) have been determined to be pathogenic (Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Arrhythmogenic right ventricular dysplasia 8 Pathogenic:1

May 06, 2021

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with arrhythmogenic right ventricular dysplasia 8 (MIM#607450) and other DSP-related cardiac disorders (OMIM). (I) 0108 - This gene is associated with both recessive and dominant disease. Variants in this gene are usually inherited in a dominant manner, however rare reports of recessive inheritance have resulted in a more severe cardiac phenotype (OMIM). (I) 0115 - Variants in this gene are known to have variable expressivity (PMID: 29062697). (I) 0205 - Variant is predicted to result in a truncated protein (premature termination codon is NOT located at least 54 nucleotides upstream of the final exon-exon junction) with less than 1/3 of the protein sequence affected. (SP) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a condition (13 heterozygotes, 0 homozygotes). (SP) 0601 - Variant results in the loss of the well-established functional C-terminal EGFP, PRD2/B and PRD3/C domains (PMID: 30354334). (SP) 0701 - Other protein truncating variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. These variants have been reported as pathogenic, and observed in individuals with arrhythmogenic right ventricular dysplasia (ARVC) and dilated cardiomyopathy (DCM) (Decipher, ClinVar). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been described as likely pathogenic (ClinVar) and as a founder variant within the Finnish population. It has been observed in multiple heterozygous individuals with DCM, arrhythmogenic cardiomyopathy and sudden cardiac death (PMID: 32005173). It has also been found in two compound heterozygous children with DCM, woolly hair and keratoderma (PMID: 19924139, PMID: 24341478). (SP) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

not provided Pathogenic:1

Jun 27, 2023

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Observed with a second DSP variant in trans in individuals with cardiomyopathy, skin and hair phenotypes, and immunohistochemistry on a skin biopsy consistent with loss of desmoplakin expression (PMID: 24341478, 19924139); Segregates with disease in many affected individuals from several families with DCM and/or other DSP-related features in published literature, and is suggested to be a founder variant in the Finnish population (PMID: 37008330, 32005173); Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 34400560, 35445468, 36142674, 29633331, 19924139, 33132336, 34343150, 35653365, 26084686, 36580316, 32005173, 37008330, 24341478) -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs730880092; hg19: chr6-7583804;