NM_004360.5(CDH1):c.1636G>A (p.Ala546Thr) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 19, 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:: RCV000217485.5

Allele description [Variation Report for NM_004360.5(CDH1):c.1636G>A (p.Ala546Thr)]

NM_004360.5(CDH1):c.1636G>A (p.Ala546Thr)

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.1636G>A (p.Ala546Thr)

HGVS:

NC_000016.10:g.68819350G>A
NG_008021.1:g.87059G>A
NM_001317184.2:c.1453G>A
NM_001317185.2:c.88G>A
NM_001317186.2:c.-254-2651G>A
NM_004360.5:c.1636G>AMANE SELECT
NP_001304113.1:p.Ala485Thr
NP_001304114.1:p.Ala30Thr
NP_004351.1:p.Ala546Thr
LRG_301t1:c.1636G>A
LRG_301:g.87059G>A
NC_000016.9:g.68853253G>A
NM_004360.3:c.1636G>A

Protein change:

A30T

Links:

dbSNP: rs876658877

NCBI 1000 Genomes Browser:

rs876658877

Molecular consequence:

NM_001317186.2:c.-254-2651G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001317184.2:c.1453G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001317185.2:c.88G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.1636G>A - 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
SCV000274684	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jul 19, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000274684

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jul 19, 2023)

germline

clinical testing

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

Details of each submission

From Ambry Genetics, SCV000274684.8

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

Description

The p.A546T variant (also known as c.1636G>A), located in coding exon 11 of the CDH1 gene, results from a G to A substitution at nucleotide position 1636. The alanine at codon 546 is replaced by threonine, an amino acid with similar properties. This amino acid position is not 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: May 1, 2024

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