rs727504443
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_ModeratePP3_StrongPP5_Very_Strong
The NM_004415.4(DSP):c.939+1G>A variant causes a splice donor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000496 in 1,613,744 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Consequence
NM_004415.4 splice_donor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DSP | NM_004415.4 | c.939+1G>A | splice_donor_variant | ENST00000379802.8 | |||
DSP | NM_001008844.3 | c.939+1G>A | splice_donor_variant | ||||
DSP | NM_001319034.2 | c.939+1G>A | splice_donor_variant | ||||
DSP | NM_001406591.1 | c.939+1G>A | splice_donor_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DSP | ENST00000379802.8 | c.939+1G>A | splice_donor_variant | 1 | NM_004415.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152088Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461656Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727136
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152088Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74284
ClinVar
Submissions by phenotype
not provided Pathogenic:4
Pathogenic, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely pathogenic, no assertion criteria provided | provider interpretation | Stanford Center for Inherited Cardiovascular Disease, Stanford University | Nov 02, 2016 | c.939+1G>A in DSP (NM_004415.2) Seen in a family with familial DCM. Testing done at Invitae. Given that this type of variation is typically pathogenic in this gene, the supporting experimental data, case data, and rarity, we consider this variant likely pathogenic and we feel it is suitable for assessing risk in healthy relatives ("predictive genetic testing"). Given that splice variants are known to be pathogenic in DSP and this specific variant has in vitro evidence for aberrant splicing, we did not do a thorough independent review of the data on the variant. Per the lab report, the variant "as been reported in the literature in patients with palmoplantar keratoderma, left dominant arrhythmogenic cardiomyopathy, arrhythmogenic right ventricular dysplasia, and dilated cardiomyopathy (PMID: 10594734, 19095136, 20864495, 24503780)." There is no variation at this nucleotide listed in the ExAC, which currently includes variant calls on >60,000 unrelated individuals of African, Asian, European, Latino, and Ashkenazi descent. The average coverage at that site in ExAC is >50x. - |
Pathogenic, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jan 05, 2023 | Canonical splice site variant expected to result in aberrant splicing; Published functional studies demonstrate aberrant splicing leading to retention of the entire intron 7, which contains a premature termination codon within the N-terminal domain of the peptide (Whittock et al., 1999); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 20738328, 25163546, 19095136, 24503780, 27532257, 10594734, 31317183, 32372669, 31402444, 31447099, 34352074, 30847666, 34135346, 20864495) - |
Primary dilated cardiomyopathy;C0349788:Arrhythmogenic right ventricular cardiomyopathy Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 05, 2015 | The c.939+1G>A variant in DSP has been reported in 2 individuals with ARVC, 1 wi th LDAC and 1 with palmoplantar hyperkeratosis (unknown cardiac status) (Whittoc k 1999, Sen Chowdry 2008, Christensen 2010, Asimaki 2009-refered to as 1218+1G>A ). This variant has been identified by our laboratory in 1 individual with DCM a nd segregated with disease in 1 affected relative. It was absent from large popu lation studies. This variant occurs in the invariant region (+/- 1,2) of the spl ice consensus sequence and studies have shown that it alters splicing, leading t o retention of intron 7 and a premature termination codon (Whittock 1999). Splic e site and other loss of function variants in DSP have been reported in patients with ARVC (http://arvcdatabase.info/). In summary, although additional studies are required to fully establish its clinical significance, the c.939+1G>A varian t is likely pathogenic. - |
Arrhythmogenic right ventricular dysplasia 8;C1854063:Arrhythmogenic cardiomyopathy with wooly hair and keratoderma Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | This sequence change affects a donor splice site in intron 7 of the DSP gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs727504443, gnomAD 0.01%). Disruption of this splice site has been observed in individual(s) with arrhythmogenic right ventricular dysplasia, dilated cardiomyopathy, left dominant arrhythmogenic cardiomyopathy, and/or palmoplantar keratoderma (PMID: 10594734, 19095136, 20864495, 24503780). ClinVar contains an entry for this variant (Variation ID: 178282). Studies have shown that disruption of this splice site results in the retention of intron 7 and introduces a premature termination codon (PMID: 10594734). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. - |
Arrhythmogenic right ventricular cardiomyopathy Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute | - | - - |
Cardiomyopathy Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario | Aug 02, 2022 | - - |
Arrhythmogenic right ventricular dysplasia 8 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 2010 | - - |
Keratosis palmoplantaris striata 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 2010 | - - |
Cardiovascular phenotype Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 15, 2023 | The c.939+1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide after coding exon 7 of the DSP gene. This mutation was identified in a family with striate palmoplantar keratoderma; six individuals were heterozygous with 3 symptomatic. This mutation was identified in individuals with dilated cardiomyopathy and arrhythmogenic right ventricular cardiomyopathy; some individuals also had variants in other cardiac-related genes (Sen-Chowdhry S et al. J. Am. Coll. Cardiol., 2008 Dec;52:2175-87; Christensen AH et al. J. Med. Genet., 2010 Nov;47:736-44; Pugh TJ et al. Genet. Med., 2014 Aug;16:601-8; Haas J et al. Eur. Heart J., 2015 May;36:1123-35a; Walsh R et al. Genet. Med., 2017 02;19:192-203). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. In addition, RNA studies have suggested that this variant results in aberrant splicing and nonsense-mediated decay (Whittock NV et al. J. Invest. Dermatol., 1999 Dec;113:940-6). Alterations in DSP that result in haploinsufficiency or protein truncation have been reported in patients with arrhythmogenic right ventricular cardiomyopathy (ARVC) and dilated cardiomyopathy (DCM) (Fressart V et al. Europace.2010;12(6):861-8; Elliott P et al. Circ Cardiovasc Genet. 2010;3(4):314-22; Quarta G et al. Circulation. 2011;123(23):2701-9; Garcia-Pavia P et al. Heart. 2011;97(21):1744-52; Rasmussen TB et al. Clin Genet.2013;84(1):20-30; Pugh TJ et al.Genet Med.2014;16(8):601-8). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at