NM_152594.3(SPRED1):c.774T>G (p.Tyr258Ter) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Sep 11, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000760726.1

Allele description [Variation Report for NM_152594.3(SPRED1):c.774T>G (p.Tyr258Ter)]

NM_152594.3(SPRED1):c.774T>G (p.Tyr258Ter)

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.774T>G (p.Tyr258Ter)
HGVS:
  • NC_000015.10:g.38351103T>G
  • NG_008980.1:g.103253T>G
  • NM_152594.3:c.774T>GMANE SELECT
  • NP_689807.1:p.Tyr258Ter
  • NC_000015.9:g.38643304T>G
  • NM_152594.2:c.774T>G
Protein change:
Y258*
Links:
dbSNP: rs1566876690
NCBI 1000 Genomes Browser:
rs1566876690
Molecular consequence:
  • NM_152594.3:c.774T>G - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000890618GeneDxcriteria provided, single submitter
Likely pathogenic
(Sep 11, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000890618.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The Y258X variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The variant is not observed in large population cohorts (Lek et al., 2016). The variant is predicted to cause loss of normal protein function through protein truncation. We consider this variant to be likely pathogenic.

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

Last Updated: Feb 27, 2021

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