NM_001164508.2(NEB):c.11613del (p.Lys3871fs) AND Nemaline myopathy 2

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 8, 2019
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:: RCV001067346.5

Allele description [Variation Report for NM_001164508.2(NEB):c.11613del (p.Lys3871fs)]

NM_001164508.2(NEB):c.11613del (p.Lys3871fs)

Gene:

NEB:nebulin [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2q23.3

Genomic location:

Preferred name:

NM_001164508.2(NEB):c.11613del (p.Lys3871fs)

HGVS:

NC_000002.12:g.151612380del
NG_009382.2:g.127110del
NM_001164507.2:c.11613del
NM_001164508.2:c.11613delMANE SELECT
NM_001271208.2:c.11613del
NM_004543.5:c.10884del
NP_001157979.2:p.Lys3871fs
NP_001157980.2:p.Lys3871fs
NP_001258137.2:p.Lys3871fs
NP_004534.3:p.Lys3628fs
LRG_202t1:c.11613del
LRG_202:g.127110del
NC_000002.11:g.152468892del
NC_000002.11:g.152468894del
NM_001271208.1:c.11613del

Protein change:

K3628fs

Links:

dbSNP: rs2098013713

NCBI 1000 Genomes Browser:

rs2098013713

Molecular consequence:

NM_001164507.2:c.11613del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001164508.2:c.11613del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001271208.2:c.11613del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004543.5:c.10884del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Nemaline myopathy 2 (NEM2)
Synonyms:: Nemaline myopathy caused by mutation in the nebulin gene; Nemaline myopathy 2, autosomal recessive
Identifiers:: MONDO: MONDO:0009725; MedGen: C1850569; OMIM: 256030

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001232403	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 8, 2019)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25205138, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001232403

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 8, 2019)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Mutation update: the spectra of nebulin variants and associated myopathies.

Lehtokari VL, Kiiski K, Sandaradura SA, Laporte J, Repo P, Frey JA, Donner K, Marttila M, Saunders C, Barth PG, den Dunnen JT, Beggs AH, Clarke NF, North KN, Laing NG, Romero NB, Winder TL, Pelin K, Wallgren-Pettersson C.

Hum Mutat. 2014 Dec;35(12):1418-26. doi: 10.1002/humu.22693.

PubMed [citation]

PMID:: 25205138
PMCID:: PMC4295925

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001232403.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

Loss-of-function variants in NEB are known to be pathogenic (PMID: 25205138). For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals with NEB-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Lys3871Asnfs*7) in the NEB gene. It is expected to result in an absent or disrupted protein product.

#	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: Feb 20, 2024

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