NM_152594.3(SPRED1):c.421C>T (p.Gln141Ter) AND Legius syndrome

Clinical significance:Pathogenic (Last evaluated: Sep 5, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000473065.1

Allele description [Variation Report for NM_152594.3(SPRED1):c.421C>T (p.Gln141Ter)]

NM_152594.3(SPRED1):c.421C>T (p.Gln141Ter)

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.421C>T (p.Gln141Ter)
HGVS:
  • NC_000015.10:g.38324807C>T
  • NG_008980.1:g.76957C>T
  • NM_152594.3:c.421C>TMANE SELECT
  • NP_689807.1:p.Gln141Ter
  • NC_000015.9:g.38617008C>T
  • NM_152594.2:c.421C>T
Protein change:
Q141*
Links:
dbSNP: rs1060502505
NCBI 1000 Genomes Browser:
rs1060502505
Molecular consequence:
  • NM_152594.3:c.421C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV000549916Invitaecriteria provided, single submitter
Pathogenic
(Sep 5, 2016)
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, SCV000549916.2

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

Description

This sequence change creates a premature translational stop signal at codon 141 (p.Gln141*) of the SPRED1 gene. It is expected to result in an absent or disrupted protein product. While this particular variant has not been reported in the literature, loss-of-function variants in SPRED1 are known to be pathogenic (PMID: 17704776). 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: Oct 7, 2021

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