NM_152594.3(SPRED1):c.38G>A (p.Ser13Asn) AND not specified

Clinical significance:Uncertain significance (Last evaluated: Oct 6, 2015)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000414496.1

Allele description [Variation Report for NM_152594.3(SPRED1):c.38G>A (p.Ser13Asn)]

NM_152594.3(SPRED1):c.38G>A (p.Ser13Asn)

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.38G>A (p.Ser13Asn)
HGVS:
  • NC_000015.10:g.38299378G>A
  • NG_008980.1:g.51528G>A
  • NM_152594.3:c.38G>AMANE SELECT
  • NP_689807.1:p.Ser13Asn
  • NC_000015.9:g.38591579G>A
  • NM_152594.2:c.38G>A
Protein change:
S13N
Links:
dbSNP: rs1057517922
NCBI 1000 Genomes Browser:
rs1057517922
Molecular consequence:
  • NM_152594.3:c.38G>A - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000491073GeneDxcriteria provided, single submitter
Uncertain significance
(Oct 6, 2015)
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, SCV000491073.1

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

Description

The S13N variant in the SPRED1 gene has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The S13N variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The S13N variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position that is conserved across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret S13N 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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