6-7566404-G-C

Position:

• chr6-7566404-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1 PM2

The NM_004415.4(DSP):​c.967G>C​(p.Glu323Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: DSP NM_004415.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:4
• Conservation: PhyloP100: 9.09

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]

DSP (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM1: In a repeat Spectrin 2 (size 103) in uniprot entity DESP_HUMAN there are 6 pathogenic changes around while only 1 benign (86%) in NM_004415.4
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DSP	NM_004415.4	c.967G>C	p.Glu323Gln	missense_variant	8/24	ENST00000379802.8	NP_004406.2
DSP	NM_001319034.2	c.967G>C	p.Glu323Gln	missense_variant	8/24		NP_001305963.1
DSP	NM_001008844.3	c.967G>C	p.Glu323Gln	missense_variant	8/24		NP_001008844.1
DSP	NM_001406591.1	c.967G>C	p.Glu323Gln	missense_variant	8/11		NP_001393520.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DSP	ENST00000379802.8	c.967G>C	p.Glu323Gln	missense_variant	8/24	1	NM_004415.4	ENSP00000369129.3
DSP	ENST00000418664.2	c.967G>C	p.Glu323Gln	missense_variant	8/24	1		ENSP00000396591.2
DSP	ENST00000710359.1	c.967G>C	p.Glu323Gln	missense_variant	8/24			ENSP00000518230.1
DSP	ENST00000682228.1	n.291G>C		non_coding_transcript_exon_variant	2/3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 33

Alfa AF: 0.0000468 Hom.: 0

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:4

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Jul 01, 2021	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Mar 04, 2024	Reported in cis with DSP p.(Y231C) in an individual with myocarditis and an individual with probable ARVC in the published literature (PMID: 33460606; 34552074); Observed with DSP p.(Y231C) in multiple individuals, suggesting these variants may be present in cis (on the same allele); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 34352074, 33460606) -

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

Likely pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 14, 2023

This sequence change replaces glutamic acid, which is acidic and polar, with glutamine, which is neutral and polar, at codon 323 of the DSP protein (p.Glu323Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with arrhythmogenic cardiomyopathy (PMID: 33460606; Invitae). ClinVar contains an entry for this variant (Variation ID: 385648). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

Arrhythmogenic cardiomyopathy with wooly hair and keratoderma Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

All of Us Research Program, National Institutes of Health

Apr 03, 2023

This missense variant replaces glutamic acid with glutamine at codon 323 of the DSP protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with DSP-related disorders in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Cardiovascular phenotype Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 27, 2023

The p.E323Q variant (also known as c.967G>C), located in coding exon 8 of the DSP gene, results from a G to C substitution at nucleotide position 967. The glutamic acid at codon 323 is replaced by glutamine, an amino acid with highly similar properties. This variant was reported to co-occur in cis with DSP p.Y231C in an individual with arrhythmogenic right ventricular cardiomyopathy (Scheel PJ et al. Am J Cardiol. 2021 Apr;145:128-134). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.18	D
BayesDel_noAF	Uncertain	0.010
CADD	Pathogenic	29
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.78	D;.
Eigen	Pathogenic	0.80
Eigen_PC	Pathogenic	0.80
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.94	D;D
M_CAP	Benign	0.071	D
MetaRNN	Uncertain	0.72	D;D
MetaSVM	Uncertain	0.46	D
MutationAssessor	Benign	1.5	L;L
PrimateAI	Uncertain	0.76	T
PROVEAN	Uncertain	-2.6	D;N
REVEL	Uncertain	0.50
Sift	Uncertain	0.0020	D;D
Sift4G	Pathogenic	0.0	D;D
Polyphen		1.0	D;.
Vest4		0.69
MutPred		0.35		Loss of ubiquitination at K322 (P = 0.0401);Loss of ubiquitination at K322 (P = 0.0401);
MVP		0.82
MPC		0.81
ClinPred		0.99	D
GERP RS		5.4
Varity_R		0.66
gMVP		0.66

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: rs1057522287; hg19: chr6-7566637; COSMIC: COSV65796826; COSMIC: COSV65796826;