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NM_001164508.2(NEB):c.19635C>A (p.Tyr6545Ter) AND Nemaline myopathy 2

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Feb 6, 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:
RCV001905783.4

Allele description [Variation Report for NM_001164508.2(NEB):c.19635C>A (p.Tyr6545Ter)]

NM_001164508.2(NEB):c.19635C>A (p.Tyr6545Ter)

Genes:
LOC126806373:BRD4-independent group 4 enhancer GRCh37_chr2:152410007-152411206 [Gene]
NEB:nebulin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q23.3
Genomic location:
Preferred name:
NM_001164508.2(NEB):c.19635C>A (p.Tyr6545Ter)
HGVS:
  • NC_000002.12:g.151553494G>T
  • NG_009382.2:g.185994C>A
  • NM_001164507.2:c.19635C>A
  • NM_001164508.2:c.19635C>AMANE SELECT
  • NM_001271208.1:c.19635C>A
  • NM_001271208.2:c.19635C>A
  • NM_004543.5:c.14532C>A
  • NP_001157979.2:p.Tyr6545Ter
  • NP_001157980.2:p.Tyr6545Ter
  • NP_001258137.2:p.Tyr6545Ter
  • NP_004534.3:p.Tyr4844Ter
  • LRG_202t1:c.19635C>A
  • LRG_202:g.185994C>A
  • NC_000002.11:g.152410008G>T
Protein change:
Y4844*
Links:
dbSNP: rs1335300113
NCBI 1000 Genomes Browser:
rs1335300113
Molecular consequence:
  • NM_001164507.2:c.19635C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001164508.2:c.19635C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001271208.2:c.19635C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_004543.5:c.14532C>A - nonsense - [Sequence Ontology: SO:0001587]

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002152582Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Feb 6, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002152582.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

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.Tyr6545*) in the NEB gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in NEB are known to be pathogenic (PMID: 25205138).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024