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NM_005055.5(RAPSN):c.531+1G>T AND multiple conditions

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 21, 2023
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:
RCV001379323.7

Allele description [Variation Report for NM_005055.5(RAPSN):c.531+1G>T]

NM_005055.5(RAPSN):c.531+1G>T

Gene:
RAPSN:receptor associated protein of the synapse [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
11p11.2
Genomic location:
Preferred name:
NM_005055.5(RAPSN):c.531+1G>T
HGVS:
  • NC_000011.10:g.47447811C>A
  • NG_008312.1:g.6368G>T
  • NG_008312.2:g.6325G>T
  • NM_005055.5:c.531+1G>TMANE SELECT
  • NM_032645.5:c.531+1G>T
  • NC_000011.9:g.47469363C>A
Links:
dbSNP: rs1421354085
NCBI 1000 Genomes Browser:
rs1421354085
Molecular consequence:
  • NM_005055.5:c.531+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_032645.5:c.531+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
Fetal akinesia deformation sequence 1 (FADS1)
Synonyms:
Pena Shokeir syndrome, type 1; Lethal Pena-Shokeir 1 syndrome; Pena-Shokeir syndrome type I; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0100101; MedGen: C1276035; Orphanet: 994; OMIM: 208150; Human Phenotype Ontology: HP:0001989
Name:
Congenital myasthenic syndrome 11
Synonyms:
MYASTHENIC SYNDROME, CONGENITAL, Ie; Myasthenic syndrome, congenital, 11, associated with acetylcholine receptor deficiency
Identifiers:
MONDO: MONDO:0014588; MedGen: C4225367; Orphanet: 590; OMIM: 616326

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001577109Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Sep 21, 2023) 		germlineclinical testing

PubMed (3)
[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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Congenital myasthenic syndromes: spotlight on genetic defects of neuromuscular transmission.

Müller JS, Mihaylova V, Abicht A, Lochmüller H.

Expert Rev Mol Med. 2007 Aug 9;9(22):1-20. Review.

PubMed [citation]
PMID:
17686188
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001577109.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

ClinVar contains an entry for this variant (Variation ID: 1067929). Disruption of this splice site has been observed in individual(s) with clinical features of congenital myasthenic syndrome (Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change affects a donor splice site in intron 2 of the RAPSN 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 RAPSN are known to be pathogenic (PMID: 17686188). 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