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NM_005055.5(RAPSN):c.838G>A (p.Gly280Arg) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 7, 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:
RCV000794222.3

Allele description [Variation Report for NM_005055.5(RAPSN):c.838G>A (p.Gly280Arg)]

NM_005055.5(RAPSN):c.838G>A (p.Gly280Arg)

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.838G>A (p.Gly280Arg)
HGVS:
  • NC_000011.10:g.47441685C>T
  • NG_008312.1:g.12494G>A
  • NM_005055.5:c.838G>AMANE SELECT
  • NM_032645.5:c.789+138G>A
  • NP_005046.2:p.Gly280Arg
  • NC_000011.9:g.47463237C>T
  • NM_005055.4:c.838G>A
Protein change:
G280R
Links:
dbSNP: rs1262674788
NCBI 1000 Genomes Browser:
rs1262674788
Molecular consequence:
  • NM_032645.5:c.789+138G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_005055.5:c.838G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Fetal akinesia deformation sequence 1 (FADS1)
Synonyms:
Pena-Shokeir syndrome type I; Fetal akinesia sequence
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
SCV000933616Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 7, 2022) 		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

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, SCV000933616.2

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

Description

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 280 of the RAPSN protein (p.Gly280Arg). 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 variant has not been reported in the literature in individuals affected with RAPSN-related conditions. ClinVar contains an entry for this variant (Variation ID: 641067). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: May 16, 2025