NM_004006.3(DMD):c.5016T>A (p.Asn1672Lys) AND not specified

Germline classification:: Benign/Likely benign (5 submissions)
Last evaluated:: Dec 10, 2021
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:: RCV000080638.31

Allele description [Variation Report for NM_004006.3(DMD):c.5016T>A (p.Asn1672Lys)]

NM_004006.3(DMD):c.5016T>A (p.Asn1672Lys)

Gene:

DMD:dystrophin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xp21.1

Genomic location:

Preferred name:

NM_004006.3(DMD):c.5016T>A (p.Asn1672Lys)

Other names:

p.N1672K:AAT>AAA; NM_000109.3(DMD):c.4992T>A(p.Asn1664Lys); NM_004006.2(DMD):c.5016T>A(p.Asn1672Lys); NM_004009.3(DMD):c.5004T>A(p.Asn1668Lys); NM_004010.3(DMD):c.4647T>A(p.Asn1549Lys); NM_004011.3(DMD):c.993T>A(p.Asn331Lys); NM_004012.3(DMD):c.984T>A(p.Asn328Lys)

HGVS:

NC_000023.11:g.32365029A>T
NG_012232.1:g.979581T>A
NM_000109.4:c.4992T>A
NM_004006.3:c.5016T>AMANE SELECT
NM_004009.3:c.5004T>A
NM_004010.3:c.4647T>A
NM_004011.4:c.993T>A
NM_004012.4:c.984T>A
NP_000100.3:p.Asn1664Lys
NP_003997.1:p.Asn1672Lys
NP_003997.2:p.Asn1672Lys
NP_004000.1:p.Asn1668Lys
NP_004001.1:p.Asn1549Lys
NP_004002.3:p.Asn331Lys
NP_004003.2:p.Asn328Lys
LRG_199t1:c.5016T>A
LRG_199:g.979581T>A
LRG_199p1:p.Asn1672Lys
NC_000023.10:g.32383146A>T
NM_004006.2:c.5016T>A
NM_004006.2:c.5016T>A
NM_004019.2:c.-1098200T>A

Protein change:

N1549K

Links:

dbSNP: rs16990264

NCBI 1000 Genomes Browser:

rs16990264

Molecular consequence:

NM_000109.4:c.4992T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004006.3:c.5016T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004009.3:c.5004T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004010.3:c.4647T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004011.4:c.993T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004012.4:c.984T>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000112540	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Benign (Jan 25, 2016)	germline	clinical testing	Citation Link,
SCV000268962	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Mar 20, 2015)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 23299917, 12354438, 19937601, 24033266
SCV000309936	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001879911	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics criteria)	Benign (Apr 23, 2021)	unknown	clinical testing	PubMed (5) [See all records that cite these PMIDs] 12354438, 23299917, 27896284, 19959795, 26467025
SCV002050948	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (Dec 10, 2021)	germline	clinical testing	Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	7	7	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	6	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Mutational spectrum of DMD mutations in dystrophinopathy patients: application of modern diagnostic techniques to a large cohort.

Flanigan KM, Dunn DM, von Niederhausern A, Soltanzadeh P, Gappmaier E, Howard MT, Sampson JB, Mendell JR, Wall C, King WM, Pestronk A, Florence JM, Connolly AM, Mathews KD, Stephan CM, Laubenthal KS, Wong BL, Morehart PJ, Meyer A, Finkel RS, Bonnemann CG, Medne L, et al.

Hum Mutat. 2009 Dec;30(12):1657-66. doi: 10.1002/humu.21114.

PubMed [citation]

PMID:: 19937601
PMCID:: PMC3404892

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

See all PubMed Citations (8)

Details of each submission

From Eurofins Ntd Llc (ga), SCV000112540.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	6	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	unknown	not provided	not provided	not provided		6	not provided	not provided	not provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000268962.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	7	not provided	not provided	clinical testing	PubMed (4)

Description

p.Asn1672Lys in exon 35 of DMD: This variant is not expected to have clinical si gnificance because it has been identified in 7.2% (760/10546) of African chromos omes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs16990261).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		7	not provided	7	not provided

From PreventionGenetics, part of Exact Sciences, SCV000309936.1

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

#	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 Athena Diagnostics, SCV001879911.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

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

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002050948.1

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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