NM_152594.3(SPRED1):c.304dup (p.Thr102fs) AND Legius syndrome

Clinical significance:Pathogenic (Last evaluated: Oct 23, 2018)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000645296.4

Allele description [Variation Report for NM_152594.3(SPRED1):c.304dup (p.Thr102fs)]

NM_152594.3(SPRED1):c.304dup (p.Thr102fs)

Gene:
SPRED1:sprouty related EVH1 domain containing 1 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
15q14
Genomic location:
Preferred name:
NM_152594.3(SPRED1):c.304dup (p.Thr102fs)
HGVS:
  • NC_000015.10:g.38322337dup
  • NG_008980.1:g.74487dup
  • NM_152594.3:c.304dupMANE SELECT
  • NP_689807.1:p.Thr102fs
  • NC_000015.9:g.38614538dup
  • NM_152594.2:c.304dupA
Protein change:
T102fs
Links:
dbSNP: rs1555391053
NCBI 1000 Genomes Browser:
rs1555391053
Molecular consequence:
  • NM_152594.3:c.304dup - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000767039Invitaecriteria provided, single submitter
Pathogenic
(Oct 23, 2018)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV000782324Center for Human Genetics, Inc,Center for Human Genetics, Inccriteria provided, single submitter
Pathogenic
(Nov 1, 2016)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Legius syndrome in fourteen families.

Denayer E, Chmara M, Brems H, Kievit AM, van Bever Y, Van den Ouweland AM, Van Minkelen R, de Goede-Bolder A, Oostenbrink R, Lakeman P, Beert E, Ishizaki T, Mori T, Keymolen K, Van den Ende J, Mangold E, Peltonen S, Brice G, Rankin J, Van Spaendonck-Zwarts KY, Yoshimura A, Legius E.

Hum Mutat. 2011 Jan;32(1):E1985-98. doi: 10.1002/humu.21404.

PubMed [citation]
PMID:
21089071
PMCID:
PMC3038325

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
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV000767039.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This sequence change creates a premature translational stop signal (p.Thr102Asnfs*7) in the SPRED1 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been reported in a family affected with Legius syndrome (PMID: 21089071). 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

From Center for Human Genetics, Inc,Center for Human Genetics, Inc, SCV000782324.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 7, 2021

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