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NM_004360.5(CDH1):c.13A>G (p.Ser5Gly) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Oct 23, 2023
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:
RCV002395361.2

Allele description [Variation Report for NM_004360.5(CDH1):c.13A>G (p.Ser5Gly)]

NM_004360.5(CDH1):c.13A>G (p.Ser5Gly)

Gene:
CDH1:cadherin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q22.1
Genomic location:
Preferred name:
NM_004360.5(CDH1):c.13A>G (p.Ser5Gly)
HGVS:
  • NC_000016.10:g.68737428A>G
  • NG_008021.1:g.5137A>G
  • NM_001317184.2:c.13A>G
  • NM_001317185.2:c.-1603A>G
  • NM_001317186.2:c.-1807A>G
  • NM_004360.5:c.13A>GMANE SELECT
  • NP_001304113.1:p.Ser5Gly
  • NP_004351.1:p.Ser5Gly
  • LRG_301t1:c.13A>G
  • LRG_301:g.5137A>G
  • NC_000016.9:g.68771331A>G
  • NM_004360.3:c.13A>G
Protein change:
S5G
Links:
dbSNP: rs1555509637
NCBI 1000 Genomes Browser:
rs1555509637
Molecular consequence:
  • NM_001317185.2:c.-1603A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317186.2:c.-1807A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001317184.2:c.13A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004360.5:c.13A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002697718Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(Oct 23, 2023) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV002697718.2

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

Description

The p.S5G variant (also known as c.13A>G), located in coding exon 1 of the CDH1 gene, results from an A to G substitution at nucleotide position 13. The serine at codon 5 is replaced by glycine, an amino acid with similar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 4400 samples (8800 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.001% (greater than 105,000 alleles tested) in our clinical cohort. This amino acid position is poorly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of p.S5G remains unclear.

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

Last Updated: May 7, 2024