NM_004006.3(DMD):c.5047A>G (p.Thr1683Ala) AND Duchenne muscular dystrophy

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 18, 2022
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:: RCV001924637.5

Allele description [Variation Report for NM_004006.3(DMD):c.5047A>G (p.Thr1683Ala)]

NM_004006.3(DMD):c.5047A>G (p.Thr1683Ala)

Gene:

DMD:dystrophin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp21.1

Genomic location:

Preferred name:

NM_004006.3(DMD):c.5047A>G (p.Thr1683Ala)

HGVS:

NC_000023.11:g.32364689T>C
NG_012232.1:g.979921A>G
NM_000109.4:c.5023A>G
NM_004006.3:c.5047A>GMANE SELECT
NM_004009.3:c.5035A>G
NM_004010.3:c.4678A>G
NM_004011.4:c.1024A>G
NM_004012.4:c.1015A>G
NP_000100.3:p.Thr1675Ala
NP_003997.2:p.Thr1683Ala
NP_004000.1:p.Thr1679Ala
NP_004001.1:p.Thr1560Ala
NP_004002.3:p.Thr342Ala
NP_004003.2:p.Thr339Ala
LRG_199:g.979921A>G
NC_000023.10:g.32382806T>C

Protein change:

T1560A

Links:

dbSNP: rs1057515873

NCBI 1000 Genomes Browser:

rs1057515873

Molecular consequence:

NM_000109.4:c.5023A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004006.3:c.5047A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004009.3:c.5035A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004010.3:c.4678A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004011.4:c.1024A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004012.4:c.1015A>G - 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
SCV002151464	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 18, 2022)	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

SCV002151464

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 18, 2022)

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, SCV002151464.2

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

Description

This sequence change replaces threonine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 1683 of the DMD protein (p.Thr1683Ala). This variant is present in population databases (no rsID available, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with DMD-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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.

#	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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