NM_004360.5(CDH1):c.866C>T (p.Ala289Val) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Dec 20, 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:: RCV003237761.10

Allele description [Variation Report for NM_004360.5(CDH1):c.866C>T (p.Ala289Val)]

NM_004360.5(CDH1):c.866C>T (p.Ala289Val)

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.866C>T (p.Ala289Val)

Other names:

NM_004360.5(CDH1):c.866C>T; p.Ala289Val

HGVS:

NC_000016.10:g.68811717C>T
NG_008021.1:g.79426C>T
NM_001317184.2:c.866C>T
NM_001317185.2:c.-750C>T
NM_001317186.2:c.-954C>T
NM_004360.4:c.866C>T
NM_004360.5:c.866C>TMANE SELECT
NP_001304113.1:p.Ala289Val
NP_004351.1:p.Ala289Val
LRG_301t1:c.866C>T
LRG_301:g.79426C>T
NC_000016.9:g.68845620C>T
NM_004360.3:c.866C>T

Protein change:

A289V

Links:

dbSNP: rs780399325

NCBI 1000 Genomes Browser:

rs780399325

Molecular consequence:

NM_001317185.2:c.-750C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317186.2:c.-954C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317184.2:c.866C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.866C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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putative Cysteine-rich venom protein LIO1 [Hypsibius exemplaris]
putative Cysteine-rich venom protein LIO1 [Hypsibius exemplaris]
gi|1174757576|gb|OQV25518.1||gnl|WG J|BV898_00458.1

Protein
Homo sapiens chromosome 16 open reading frame 61, mRNA (cDNA clone MGC:45036 IMA...
Homo sapiens chromosome 16 open reading frame 61, mRNA (cDNA clone MGC:45036 IMAGE:5399193), complete cds
gi|21595752|gb|BC032631.1|

Nucleotide
F1PDQ3 (0)
Protein
SRP059825 (23)
SRA

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002009846	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 3, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005327370	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Dec 20, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002009846

Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 3, 2021)

germline

clinical testing

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

SCV005327370

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Dec 20, 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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	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 Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden, SCV002009846.3

#	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	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From GeneDx, SCV005327370.1

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

Description

Observed in individuals with breast cancer (PMID: 36436516, 30287823); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 30287823, 36243179, 36436516, 15235021, 22850631)

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

Last Updated: Oct 13, 2024

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