NM_004360.5(CDH1):c.1670A>G (p.Lys557Arg) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 23, 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:: RCV001773651.3

Allele description [Variation Report for NM_004360.5(CDH1):c.1670A>G (p.Lys557Arg)]

NM_004360.5(CDH1):c.1670A>G (p.Lys557Arg)

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.1670A>G (p.Lys557Arg)

HGVS:

NC_000016.10:g.68819384A>G
NG_008021.1:g.87093A>G
NM_001317184.2:c.1487A>G
NM_001317185.2:c.122A>G
NM_001317186.2:c.-254-2617A>G
NM_004360.5:c.1670A>GMANE SELECT
NP_001304113.1:p.Lys496Arg
NP_001304114.1:p.Lys41Arg
NP_004351.1:p.Lys557Arg
LRG_301t1:c.1670A>G
LRG_301:g.87093A>G
NC_000016.9:g.68853287A>G
NM_004360.3:c.1670A>G

Protein change:

K41R

Links:

dbSNP: rs1173188736

NCBI 1000 Genomes Browser:

rs1173188736

Molecular consequence:

NM_001317186.2:c.-254-2617A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001317184.2:c.1487A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001317185.2:c.122A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.1670A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002004520	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (May 23, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002004520

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(May 23, 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

Details of each submission

From GeneDx, SCV002004520.3

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

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 15235021, 22850631, 33237286)

#	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: Sep 29, 2024

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