NM_004360.5(CDH1):c.79C>T (p.Pro27Ser) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 17, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000582299.9

Allele description [Variation Report for NM_004360.5(CDH1):c.79C>T (p.Pro27Ser)]

NM_004360.5(CDH1):c.79C>T (p.Pro27Ser)

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.79C>T (p.Pro27Ser)

Other names:

NM_004360.4(CDH1):c.79C>T

HGVS:

NC_000016.10:g.68738327C>T
NG_008021.1:g.6036C>T
NM_001317184.2:c.79C>T
NM_001317185.2:c.-1537C>T
NM_001317186.2:c.-1741C>T
NM_004360.5:c.79C>TMANE SELECT
NP_001304113.1:p.Pro27Ser
NP_004351.1:p.Pro27Ser
LRG_301t1:c.79C>T
LRG_301:g.6036C>T
NC_000016.9:g.68772230C>T
NM_004360.3:c.79C>T
NM_004360.4:c.79C>T

Protein change:

P27S

Links:

dbSNP: rs878854696

NCBI 1000 Genomes Browser:

rs878854696

Molecular consequence:

NM_001317185.2:c.-1537C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317186.2:c.-1741C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317184.2:c.79C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.79C>T - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000689566	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 5, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 26182300, 25741868
SCV002678650	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jul 17, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 26182300, 35264596, 36436516 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000689566

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jul 5, 2022)

germline

clinical testing

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

SCV002678650

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jul 17, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Hereditary Diffuse Gastric Cancer Syndrome: CDH1 Mutations and Beyond.

Hansford S, Kaurah P, Li-Chang H, Woo M, Senz J, Pinheiro H, Schrader KA, Schaeffer DF, Shumansky K, Zogopoulos G, Santos TA, Claro I, Carvalho J, Nielsen C, Padilla S, Lum A, Talhouk A, Baker-Lange K, Richardson S, Lewis I, Lindor NM, Pennell E, et al.

JAMA Oncol. 2015 Apr;1(1):23-32. doi: 10.1001/jamaoncol.2014.168. Erratum in: JAMA Oncol. 2015 Apr;1(1):110. doi: 10.1001/jamaoncol.2015.0410.

PubMed [citation]

PMID:: 26182300

See all PubMed Citations (4)

Details of each submission

From Color Diagnostics, LLC DBA Color Health, SCV000689566.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This missense variant replaces proline with serine at codon 27 of the CDH1 protein. To our knowledge, functional studies have not been reported for this variant. This variant has been reported in an individual affected with HDGC-associated cancer and in a related unaffected individual (PMID: 26182300). This variant has been identified in 1/156646 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Ambry Genetics, SCV002678650.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

The p.P27S variant (also known as c.79C>T), located in coding exon 2 of the CDH1 gene, results from a C to T substitution at nucleotide position 79. The proline at codon 27 is replaced by serine, an amino acid with similar properties. This alteration was reported in an unaffected obligate carrier from a family with an isolated individual diagnosed with diffuse gastric cancer before age 40 (Hansford S et al. JAMA Oncol, 2015 Apr;1:23-32). This alteration was also detected in a cohort of 1663 Brazilian breast cancer patients who underwent hereditary multigene panel testing (Guindalini RSC et al. Sci Rep, 2022 Mar;12:4190). Additionally, this alteration was identified in an individual with a family history of gastric cancer (Garcia-Pelaez J et al. Lancet Oncol, 2023 Jan;24:91-106). This amino acid position is well 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 this alteration remains unclear.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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