NM_004006.3(DMD):c.6120T>A (p.Asn2040Lys) AND Duchenne muscular dystrophy

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 20, 2021
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV002012324.6

Allele description [Variation Report for NM_004006.3(DMD):c.6120T>A (p.Asn2040Lys)]

NM_004006.3(DMD):c.6120T>A (p.Asn2040Lys)

Gene:

DMD:dystrophin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp21.1

Genomic location:

Preferred name:

NM_004006.3(DMD):c.6120T>A (p.Asn2040Lys)

HGVS:

NC_000023.11:g.32287699A>T
NG_012232.1:g.1056911T>A
NM_000109.4:c.6096T>A
NM_004006.3:c.6120T>AMANE SELECT
NM_004009.3:c.6108T>A
NM_004010.3:c.5751T>A
NM_004011.4:c.2097T>A
NM_004012.4:c.2088T>A
NP_000100.3:p.Asn2032Lys
NP_003997.2:p.Asn2040Lys
NP_004000.1:p.Asn2036Lys
NP_004001.1:p.Asn1917Lys
NP_004002.3:p.Asn699Lys
NP_004003.2:p.Asn696Lys
LRG_199:g.1056911T>A
NC_000023.10:g.32305816A>T

Protein change:

N1917K

Links:

dbSNP: rs1409711434

NCBI 1000 Genomes Browser:

rs1409711434

Molecular consequence:

NM_000109.4:c.6096T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004006.3:c.6120T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004009.3:c.6108T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004010.3:c.5751T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004011.4:c.2097T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004012.4:c.2088T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Duchenne muscular dystrophy (DMD)
Synonyms:: Muscular dystrophy, pseudohypertrophic progressive, Duchenne type
Identifiers:: MONDO: MONDO:0010679; MedGen: C0013264; Orphanet: 98896; OMIM: 310200

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002232834	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 20, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002232834

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 20, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002232834.3

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with DMD-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces asparagine with lysine at codon 2040 of the DMD protein (p.Asn2040Lys). The asparagine residue is highly conserved and there is a moderate physicochemical difference between asparagine and lysine.

#	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

Last Updated: Nov 10, 2024

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