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NM_152594.3(SPRED1):c.841C>T (p.Gln281Ter) AND Legius syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 11, 2020
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:
RCV001386578.7

Allele description [Variation Report for NM_152594.3(SPRED1):c.841C>T (p.Gln281Ter)]

NM_152594.3(SPRED1):c.841C>T (p.Gln281Ter)

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.841C>T (p.Gln281Ter)
HGVS:
  • NC_000015.10:g.38351170C>T
  • NG_008980.1:g.103320C>T
  • NM_152594.3:c.841C>TMANE SELECT
  • NP_689807.1:p.Gln281Ter
  • NC_000015.9:g.38643371C>T
Protein change:
Q281*
Links:
dbSNP: rs755557783
NCBI 1000 Genomes Browser:
rs755557783
Molecular consequence:
  • NM_152594.3:c.841C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001586841Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Oct 11, 2020) 		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, SCV001586841.4

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

Description

This sequence change results in a premature translational stop signal in the SPRED1 gene (p.Gln281*). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 164 amino acid(s) of the SPRED1 protein. This variant is present in population databases (rs755557783, ExAC no frequency). For these reasons, this variant has been classified as Pathogenic. This variant disrupts the C-terminus of the SPRED1 protein. Other variant(s) that disrupt this region (p.Ser411Tyrfs*10) have been determined to be pathogenic (Invitae). This suggests that variants that disrupt this region of the protein are likely to be causative of disease. This variant has not been reported in the literature in individuals with SPRED1-related conditions.

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

Last Updated: Sep 29, 2024