NM_004360.5(CDH1):c.1687G>T (p.Ala563Ser) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Feb 25, 2021
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:: RCV000130507.11

Allele description [Variation Report for NM_004360.5(CDH1):c.1687G>T (p.Ala563Ser)]

NM_004360.5(CDH1):c.1687G>T (p.Ala563Ser)

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.1687G>T (p.Ala563Ser)

Other names:

p.A563S:GCC>TCC

HGVS:

NC_000016.10:g.68819401G>T
NG_008021.1:g.87110G>T
NM_001317184.2:c.1504G>T
NM_001317185.2:c.139G>T
NM_001317186.2:c.-254-2600G>T
NM_004360.5:c.1687G>TMANE SELECT
NP_001304113.1:p.Ala502Ser
NP_001304114.1:p.Ala47Ser
NP_004351.1:p.Ala563Ser
LRG_301t1:c.1687G>T
LRG_301:g.87110G>T
NC_000016.9:g.68853304G>T
NM_004360.3:c.1687G>T
NM_004360.4:c.1687G>T
p.A563S

Protein change:

A47S

Links:

dbSNP: rs587782044

NCBI 1000 Genomes Browser:

rs587782044

Molecular consequence:

NM_001317186.2:c.-254-2600G>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001317184.2:c.1504G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001317185.2:c.139G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.1687G>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

Recent activity

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dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodie...
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1A isoform X4 [Homo sapiens]
gi|2217328693|ref|XP_047300644.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000185376	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Feb 25, 2021)	germline	clinical testing	Citation Link,
SCV000684375	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Apr 5, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000185376

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Feb 25, 2021)

germline

clinical testing

Citation Link,

SCV000684375

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Apr 5, 2019)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Details of each submission

From Ambry Genetics, SCV000185376.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The p.A563S variant (also known as c.1687G>T), located in coding exon 11 of the CDH1 gene, results from a G to T substitution at nucleotide position 1687. The alanine at codon 563 is replaced by serine, an amino acid with similar properties. 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

From Color Diagnostics, LLC DBA Color Health, SCV000684375.3

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

#	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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