NM_152594.3(SPRED1):c.124G>A (p.Val42Ile) AND not specified

Clinical significance:Likely benign (Last evaluated: Jul 26, 2012)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000041238.4

Allele description [Variation Report for NM_152594.3(SPRED1):c.124G>A (p.Val42Ile)]

NM_152594.3(SPRED1):c.124G>A (p.Val42Ile)

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.124G>A (p.Val42Ile)
Other names:
p.V42I:GTC>ATC
HGVS:
  • NC_000015.10:g.38299464G>A
  • NG_008980.1:g.51614G>A
  • NM_152594.3:c.124G>AMANE SELECT
  • NP_689807.1:p.Val42Ile
  • NC_000015.9:g.38591665G>A
  • NM_152594.2:c.124G>A
  • c.124G>A
Protein change:
V42I
Links:
dbSNP: rs147204964
NCBI 1000 Genomes Browser:
rs147204964
Molecular consequence:
  • NM_152594.3:c.124G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000064929Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicinecriteria provided, single submitter
Likely benign
(Jul 26, 2012)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided21not providednot providednot providedclinical testing

Citations

PubMed

Identification of SPRED1 deletions using RT-PCR, multiplex ligation-dependent probe amplification and quantitative PCR.

Spencer E, Davis J, Mikhail F, Fu C, Vijzelaar R, Zackai EH, Feret H, Meyn MS, Shugar A, Bellus G, Kocsis K, Kivirikko S, Pöyhönen M, Messiaen L.

Am J Med Genet A. 2011 Jun;155A(6):1352-9. doi: 10.1002/ajmg.a.33894. Epub 2011 May 5.

PubMed [citation]
PMID:
21548021

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine, SCV000064929.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (2)

Description

Val42Ile in exon 02 of SPRED1: The Val42Ile variant in SPRED1 was reported in on e individual with Legius syndrome (Spencer 2011). Furthermore, this variant was identified in one individual with clinical features within the Noonan spectrum b y our laboratory but was also found in an unaffected parent. However, this prob and also carried a BRAF variant that likely occurred de novo because it was not found in either parent of the proband. In addition, this variant has been identi fied in 0.07% (3/4400) of African American chromosomes from a broad population b y the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS/; dbSNP r s147204964). Computational analyses (biochemical amino acid properties, conserv ation, AlignGVGD, PolyPhen2, and SIFT) do not provide strong support for or agai nst an impact to the protein. In summary, the Val42Ile variant is likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided2not provided1not provided

Last Updated: Nov 27, 2021

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