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NM_000080.4(CHRNE):c.802+1G>A AND Congenital myasthenic syndrome 4A

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 3, 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:
RCV003842476.2

Allele description [Variation Report for NM_000080.4(CHRNE):c.802+1G>A]

NM_000080.4(CHRNE):c.802+1G>A

Genes:
CHRNE:cholinergic receptor nicotinic epsilon subunit [Gene - OMIM - HGNC]
C17orf107:chromosome 17 open reading frame 107 [Gene - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17p13.2
Genomic location:
Preferred name:
NM_000080.4(CHRNE):c.802+1G>A
HGVS:
  • NC_000017.11:g.4900989C>T
  • NG_008029.2:g.7087G>A
  • NM_000080.4:c.802+1G>AMANE SELECT
  • NM_001145536.2:c.*456C>TMANE SELECT
  • LRG_1254t1:c.802+1G>A
  • LRG_1254:g.7087G>A
  • NC_000017.10:g.4804284C>T
Molecular consequence:
  • NM_001145536.2:c.*456C>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_000080.4:c.802+1G>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Congenital myasthenic syndrome 4A
Synonyms:
CONGENITAL MYASTHENIC SYNDROME TYPE Ia1; Myasthenic syndrome, congenital, 4a, slow-channel; MYASTHENIC SYNDROME, CONGENITAL, 4A, SLOW-CHANNEL, AUTOSOMAL RECESSIVE
Identifiers:
MONDO: MONDO:0011600; MedGen: C4225413; Orphanet: 590; OMIM: 605809

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004650982Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Nov 3, 2022) 		germlineclinical testing

PubMed (5)
[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

Myasthenic syndromes in Turkish kinships due to mutations in the acetylcholine receptor.

Ohno K, Anlar B, Ozdirim E, Brengman JM, DeBleecker JL, Engel AG.

Ann Neurol. 1998 Aug;44(2):234-41.

PubMed [citation]
PMID:
9708546

Congenital myasthenic syndrome in Turkey: clinical and genetic features in the long-term follow-up of patients.

Gül Mert G, Özcan N, Hergüner Ö, Altunbaşak Ş, Incecik F, Bişgin A, Ceylaner S.

Acta Neurol Belg. 2021 Apr;121(2):529-534. doi: 10.1007/s13760-019-01246-9. Epub 2019 Nov 26.

PubMed [citation]
PMID:
31773638
See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004650982.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (5)

Description

Disruption of this splice site has been observed in individual(s) with autosomal recessive congenital myasthenic syndrome (PMID: 9708546, 31773638). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 7 of the CHRNE gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in CHRNE are known to be pathogenic (PMID: 22678886). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024