NM_004415.4(DSP):c.3923G>A (p.Arg1308Gln) AND not provided

Germline classification:: Benign (5 submissions)
Last evaluated:: Jul 1, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000586281.17

Allele description [Variation Report for NM_004415.4(DSP):c.3923G>A (p.Arg1308Gln)]

NM_004415.4(DSP):c.3923G>A (p.Arg1308Gln)

Gene:

DSP:desmoplakin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6p24.3

Genomic location:

Preferred name:

NM_004415.4(DSP):c.3923G>A (p.Arg1308Gln)

HGVS:

NC_000006.12:g.7580113G>A
NG_008803.1:g.43477G>A
NM_001008844.3:c.3582+341G>A
NM_001319034.2:c.3923G>A
NM_004415.4:c.3923G>AMANE SELECT
NP_001305963.1:p.Arg1308Gln
NP_004406.2:p.Arg1308Gln
LRG_423t1:c.3923G>A
LRG_423:g.43477G>A
NC_000006.11:g.7580346G>A
NM_004415.2:c.3923G>A
NM_004415.3:c.3923G>A

Protein change:

R1308Q

Links:

dbSNP: rs184154918

NCBI 1000 Genomes Browser:

rs184154918

Molecular consequence:

NM_001008844.3:c.3582+341G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001319034.2:c.3923G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004415.4:c.3923G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Transducin/WD40 repeat-like superfamily protein [Arabidopsis thaliana]
Transducin/WD40 repeat-like superfamily protein [Arabidopsis thaliana]
gi|18410015|ref|NP_566994.1|

Protein
cytochrome c oxidase subunit II (mitochondrion) [Echinops telfairi]
cytochrome c oxidase subunit II (mitochondrion) [Echinops telfairi]
gi|11994080|gnl|NCBI_MITO|COX2_1556 |NP_072060.1|COX2_15563

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000698434	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Aug 22, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV001740905	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001797614	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001866691	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Mar 3, 2015)	germline	clinical testing	Citation Link,
SCV004163052	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Jul 1, 2022)	germline	clinical testing	Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Arrhythmogenic right ventricular dysplasia: clinical characteristics and identification of novel desmosome gene mutations.

Yu CC, Yu CH, Hsueh CH, Yang CT, Juang JM, Hwang JJ, Lin JL, Lai LP.

J Formos Med Assoc. 2008 Jul;107(7):548-58. doi: 10.1016/S0929-6646(08)60168-0. Erratum in: J Formos Med Assoc. 2009 Mar;108(3):265.

PubMed [citation]

PMID:: 18632414

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000698434.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

Variant summary: The c.3923G>A (p.Arg1308Gln) in the DSP gene is a missense change that involves the alteration of a non- conserved nucleotide and 5/5 in silico tools predict benign outcome. The variant was observed in the large and broad cohorts of the ExAC project at an allele frequency of 0.001212 (146/ 120504 chrs tested), predominantly in individuals of East Asian descent (0.01648; 142/ 8618 chrs, including 1 homozygotes). The latter frequency exceeds the maximal expected allele frequency for a pathogenic variant in this gene (0.00001). Lastly, several reputable databases/diagnostic centers classified the variant of interest as Benign/Likely Benign. Taking together, the variant was classified as Benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001740905.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus, SCV001797614.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV001866691.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is associated with the following publications: (PMID: 26585738)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From CeGaT Center for Human Genetics Tuebingen, SCV004163052.9

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	not provided

Description

DSP: BP4, BS1, BS2

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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