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NM_001164508.2(NEB):c.25336C>T (p.Arg8446Ter) AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Sep 30, 2022
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:
RCV000520480.9

Allele description [Variation Report for NM_001164508.2(NEB):c.25336C>T (p.Arg8446Ter)]

NM_001164508.2(NEB):c.25336C>T (p.Arg8446Ter)

Genes:
NEB:nebulin [Gene - OMIM - HGNC]
RIF1:replication timing regulatory factor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2q23.3
Genomic location:
Preferred name:
NM_001164508.2(NEB):c.25336C>T (p.Arg8446Ter)
HGVS:
  • NC_000002.12:g.151490039G>A
  • NG_009382.2:g.249449C>T
  • NM_001164507.2:c.25336C>T
  • NM_001164508.2:c.25336C>TMANE SELECT
  • NM_001271208.2:c.25441C>T
  • NM_004543.5:c.19768C>T
  • NP_001157979.2:p.Arg8446Ter
  • NP_001157980.2:p.Arg8446Ter
  • NP_001258137.2:p.Arg8481Ter
  • NP_004534.3:p.Arg6590Ter
  • LRG_202t1:c.25441C>T
  • LRG_202:g.249449C>T
  • NC_000002.11:g.152346553G>A
  • NM_001271208.1:c.25441C>T
Protein change:
R6590*
Links:
dbSNP: rs200731870
NCBI 1000 Genomes Browser:
rs200731870
Molecular consequence:
  • NM_001164507.2:c.25336C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001164508.2:c.25336C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001271208.2:c.25441C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_004543.5:c.19768C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000617715GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Pathogenic
(Sep 30, 2022)
germlineclinical testing

Citation Link,

SCV002018257Revvity Omics, Revvity
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Nov 18, 2019)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From GeneDx, SCV000617715.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Reported in a family with nemaline myopathy who also harbored a NEB frameshift variant, but it is not known whether the variants occurred on the same (in cis) or on different (in trans) chromosomes (Lehtokari et al., 2014); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 30467404, 25205138, 30057997, 34426522, 31589614, 31127727)

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

From Revvity Omics, Revvity, SCV002018257.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024