NM_152594.3(SPRED1):c.1313G>T (p.Gly438Val) AND Legius syndrome

Clinical significance:Uncertain significance (Last evaluated: Apr 24, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001044046.1

Allele description [Variation Report for NM_152594.3(SPRED1):c.1313G>T (p.Gly438Val)]

NM_152594.3(SPRED1):c.1313G>T (p.Gly438Val)

Gene:
SPRED1:sprouty related EVH1 domain containing 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
15q14
Genomic location:
Preferred name:
NM_152594.3(SPRED1):c.1313G>T (p.Gly438Val)
HGVS:
  • NC_000015.10:g.38351642G>T
  • NG_008980.1:g.103792G>T
  • NM_152594.3:c.1313G>TMANE SELECT
  • NP_689807.1:p.Gly438Val
  • NC_000015.9:g.38643843G>T
  • NM_152594.2:c.1313G>T
Protein change:
G438V
Links:
dbSNP: rs573603750
NCBI 1000 Genomes Browser:
rs573603750
Molecular consequence:
  • NM_152594.3:c.1313G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Legius syndrome (LGSS)
Synonyms:
Neurofibromatosis type 1 like syndrome
Identifiers:
MONDO: MONDO:0012669; MedGen: C1969623; Orphanet: 137605; OMIM: 611431

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001207820Invitaecriteria provided, single submitter
Uncertain significance
(Apr 24, 2019)
germlineclinical testing

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

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001207820.2

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

Description

This sequence change replaces glycine with valine at codon 438 of the SPRED1 protein (p.Gly438Val). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and valine. This variant is present in population databases (rs573603750, ExAC 0.01%). This variant has not been reported in the literature in individuals with SPRED1-related conditions. 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: Nov 27, 2021

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