NM_004360.5(CDH1):c.1793G>A (p.Arg598Gln) AND not provided

Germline classification:: Conflicting classifications of pathogenicity (2 submissions)
Last evaluated:: Sep 18, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV001565239.10

Allele description [Variation Report for NM_004360.5(CDH1):c.1793G>A (p.Arg598Gln)]

NM_004360.5(CDH1):c.1793G>A (p.Arg598Gln)

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.1793G>A (p.Arg598Gln)

HGVS:

NC_000016.10:g.68822082G>A
NG_008021.1:g.89791G>A
NM_001317184.2:c.1610G>A
NM_001317185.2:c.245G>A
NM_001317186.2:c.-173G>A
NM_004360.5:c.1793G>AMANE SELECT
NP_001304113.1:p.Arg537Gln
NP_001304114.1:p.Arg82Gln
NP_004351.1:p.Arg598Gln
LRG_301t1:c.1793G>A
LRG_301:g.89791G>A
NC_000016.9:g.68855985G>A
NM_004360.3:c.1793G>A
NM_004360.4:c.1793G>A
P12830:p.Arg598Gln

Protein change:

R537Q

Links:

UniProtKB: P12830#VAR_001319; dbSNP: rs780759537

NCBI 1000 Genomes Browser:

rs780759537

Molecular consequence:

NM_001317186.2:c.-173G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317184.2:c.1610G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001317185.2:c.245G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.1793G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001788550	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Sep 18, 2023)	germline	clinical testing	Citation Link,
SCV004220804	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely benign (Apr 1, 2022)	unknown	clinical testing	PubMed (10) [See all records that cite these PMIDs] 30287823, 27925203, 22788692, 10896919, 10094558, 25186627, 28944238, 29641532, 33471991, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001788550

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Sep 18, 2023)

germline

clinical testing

Citation Link,

SCV004220804

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Likely benign
(Apr 1, 2022)

unknown

clinical testing

PubMed (10)
[See all records that cite these PMIDs]

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Germline pathogenic variants of 11 breast cancer genes in 7,051 Japanese patients and 11,241 controls.

Momozawa Y, Iwasaki Y, Parsons MT, Kamatani Y, Takahashi A, Tamura C, Katagiri T, Yoshida T, Nakamura S, Sugano K, Miki Y, Hirata M, Matsuda K, Spurdle AB, Kubo M.

Nat Commun. 2018 Oct 4;9(1):4083. doi: 10.1038/s41467-018-06581-8.

PubMed [citation]

PMID:: 30287823
PMCID:: PMC6172276

The genetic landscape of breast carcinomas with neuroendocrine differentiation.

Marchiò C, Geyer FC, Ng CK, Piscuoglio S, De Filippo MR, Cupo M, Schultheis AM, Lim RS, Burke KA, Guerini-Rocco E, Papotti M, Norton L, Sapino A, Weigelt B, Reis-Filho JS.

J Pathol. 2017 Feb;241(3):405-419. doi: 10.1002/path.4837. Epub 2016 Dec 26.

PubMed [citation]

PMID:: 27925203
PMCID:: PMC5481202

See all PubMed Citations (10)

Details of each submission

From GeneDx, SCV001788550.4

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

Description

In silico analysis supports that this missense variant does not alter protein structure/function; Observed in individuals with breast cancer (Tung et al., 2015; Garcia-Pelaez et al., 2023); This variant is associated with the following publications: (PMID: 10094558, 22788692, 9744472, 10896919, 27925203, 12647996, 30287823, 29641532, 28944238, 36063148, 25186627, 15235021, 22850631, 36243179, 36436516)

#	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

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV004220804.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (10)

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

Last Updated: Feb 25, 2025

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