NM_004360.5(CDH1):c.286A>T (p.Ile96Phe) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 26, 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:: RCV000165180.10

Allele description [Variation Report for NM_004360.5(CDH1):c.286A>T (p.Ile96Phe)]

NM_004360.5(CDH1):c.286A>T (p.Ile96Phe)

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.286A>T (p.Ile96Phe)

HGVS:

NC_000016.10:g.68801792A>T
NG_008021.1:g.69501A>T
NM_001317184.2:c.286A>T
NM_001317185.2:c.-1330A>T
NM_001317186.2:c.-1534A>T
NM_004360.5:c.286A>TMANE SELECT
NP_001304113.1:p.Ile96Phe
NP_004351.1:p.Ile96Phe
LRG_301t1:c.286A>T
LRG_301:g.69501A>T
NC_000016.9:g.68835695A>T
NM_004360.3:c.286A>T
NM_004360.4:c.286A>T
p.I96F

Protein change:

I96F

Links:

dbSNP: rs749306433

NCBI 1000 Genomes Browser:

rs749306433

Molecular consequence:

NM_001317185.2:c.-1330A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317186.2:c.-1534A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317184.2:c.286A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.286A>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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flap structure-specific endonuclease 1, partial [Xiphophorus kallmani]
flap structure-specific endonuclease 1, partial [Xiphophorus kallmani]
gi|461694092|gb|AGH19902.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000215892	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Aug 26, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 28580595, 33471991 Citation Link,
SCV000908711	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 17, 2020)	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

SCV000215892

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Aug 26, 2023)

germline

clinical testing

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

Citation Link,

SCV000908711

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 17, 2020)

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

Mutation screening of 10 cancer susceptibility genes in unselected breast cancer patients.

Xie Y, Li G, Chen M, Guo X, Tang L, Luo X, Wang S, Yi W, Dai L, Wang J.

Clin Genet. 2018 Jan;93(1):41-51. doi: 10.1111/cge.13063. Epub 2017 Sep 25.

PubMed [citation]

PMID:: 28580595

Breast Cancer Risk Genes - Association Analysis in More than 113,000 Women.

Breast Cancer Association Consortium., Dorling L, Carvalho S, Allen J, González-Neira A, Luccarini C, Wahlström C, Pooley KA, Parsons MT, Fortuno C, Wang Q, Bolla MK, Dennis J, Keeman R, Alonso MR, Álvarez N, Herraez B, Fernandez V, Núñez-Torres R, Osorio A, Valcich J, Li M, et al.

N Engl J Med. 2021 Feb 4;384(5):428-439. doi: 10.1056/NEJMoa1913948. Epub 2021 Jan 20.

PubMed [citation]

PMID:: 33471991
PMCID:: PMC7611105

See all PubMed Citations (3)

Details of each submission

From Ambry Genetics, SCV000215892.8

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

Description

The p.I96F variant (also known as c.286A>T), located in coding exon 3 of the CDH1 gene, results from an A to T substitution at nucleotide position 286. The isoleucine at codon 96 is replaced by phenylalanine, an amino acid with highly similar properties. This alteration has been identified in a Chinese woman diagnosed with breast cancer (Xie Y et al. Clin. Genet., 2018 Jan;93:41-51). This variant was reported in 4/60,466 breast cancer cases and in 5/53,461 controls (Dorling et al. N Engl J Med 2021 02;384:428-439). 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 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, SCV000908711.3

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

Description

This missense variant replaces isoleucine with phenylalanine at codon 96 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 breast cancer (PMID: 28580595). This variant has not been identified 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

Last Updated: Sep 29, 2024

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