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NM_005055.5(RAPSN):c.1116GAA[1] (p.Lys373del) AND RAPSN-related condition

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 3, 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:
RCV003396667.4

Allele description

NM_005055.5(RAPSN):c.1116GAA[1] (p.Lys373del)

Gene:
RAPSN:receptor associated protein of the synapse [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
11p11.2
Genomic location:
Preferred name:
NM_005055.5(RAPSN):c.1116GAA[1] (p.Lys373del)
HGVS:
  • NC_000011.10:g.47438778TCT[1]
  • NC_000011.10:g.47438778_47438780TCT[1]
  • NG_008312.1:g.15398GAA[1]
  • NM_005055.5:c.1116GAA[1]MANE SELECT
  • NM_032645.5:c.939GAA[1]
  • NP_005046.2:p.Lys373del
  • NP_116034.2:p.Lys314del
  • NC_000011.9:g.47460328_47460330del
  • NC_000011.9:g.47460329TCT[1]
  • NM_005055.4:c.1119_1121del
  • NM_005055.4:c.1119_1121delGAA
  • NM_005055.5:c.1119_1121delMANE SELECT
Protein change:
K314del
Links:
dbSNP: rs759488854
NCBI 1000 Genomes Browser:
rs759488854
Molecular consequence:
  • NM_005055.5:c.1116GAA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_032645.5:c.939GAA[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:
RAPSN-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004119618PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Oct 3, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
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 PreventionGenetics, part of Exact Sciences, SCV004119618.1

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

Description

The RAPSN c.1119_1121delGAA variant is predicted to result in an in-frame deletion (p.Lys373del). This variant has been reported along with a second RAPSN variant in several patients with congenital myasthenic syndrome, including three affected siblings in one family (Table 1, Cossins et al. 2006. PubMed ID: 16945936; Table 2, Milone et al. 2009. PubMed ID: 19620612; Table S2, Abicht et al. 2012. PubMed ID: 22678886; Internal Data, PreventionGenetics). It has also been reported in the homozygous or compound heterozygous state in two prenatal cases from families with recurrent non-immune fetal hydrops (Table 2, Zhou et al. 2021. PubMed ID: 33897756). In experimental studies, the p.Lys373del change was reported to affect RAPSN stability (Figure 3, Cossins et al. 2006. PubMed ID: 16945936). This variant is reported in 0.0011% of alleles in individuals of European (non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/11-47460327-GTTC-G). Taken together, this variant is interpreted as pathogenic.

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

Last Updated: Mar 10, 2024