NM_152594.3(SPRED1):c.66G>T (p.Met22Ile) AND not provided

Clinical significance:Uncertain significance (Last evaluated: May 23, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000658339.1

Allele description [Variation Report for NM_152594.3(SPRED1):c.66G>T (p.Met22Ile)]

NM_152594.3(SPRED1):c.66G>T (p.Met22Ile)

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.66G>T (p.Met22Ile)
HGVS:
  • NC_000015.10:g.38299406G>T
  • NG_008980.1:g.51556G>T
  • NM_152594.3:c.66G>TMANE SELECT
  • NP_689807.1:p.Met22Ile
  • NC_000015.9:g.38591607G>T
  • NM_152594.2:c.66G>T
Protein change:
M22I
Links:
dbSNP: rs1555389685
NCBI 1000 Genomes Browser:
rs1555389685
Molecular consequence:
  • NM_152594.3:c.66G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000780111GeneDxcriteria provided, single submitter
Uncertain significance
(May 23, 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, SCV000780111.2

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

Description

The M22I variant in the SPRED1 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The M22I variant is not observed in large population cohorts (Lek et al., 2016). The M22I variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. In-silico analyses, including protein predictors and evolutionary conservation, support a deleterious effect. We interpret M22I as a variant of uncertain significance.

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

Last Updated: Feb 27, 2021

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