NM_004360.5(CDH1):c.1568A>G (p.Tyr523Cys) AND not provided

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Feb 6, 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:: RCV000587509.11

Allele description [Variation Report for NM_004360.5(CDH1):c.1568A>G (p.Tyr523Cys)]

NM_004360.5(CDH1):c.1568A>G (p.Tyr523Cys)

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.1568A>G (p.Tyr523Cys)

Other names:

p.Y523C:TAT>TGT; NM_004360.5(CDH1):c.1568A>G

HGVS:

NC_000016.10:g.68819282A>G
NG_008021.1:g.86991A>G
NM_001317184.2:c.1385A>G
NM_001317185.2:c.20A>G
NM_001317186.2:c.-254-2719A>G
NM_004360.5:c.1568A>GMANE SELECT
NP_001304113.1:p.Tyr462Cys
NP_001304114.1:p.Tyr7Cys
NP_004351.1:p.Tyr523Cys
LRG_301t1:c.1568A>G
LRG_301:g.86991A>G
NC_000016.9:g.68853185A>G
NM_004360.3:c.1568A>G
NM_004360.4:c.1568A>G
p.Y523C

Protein change:

Y462C

Links:

dbSNP: rs553907248

NCBI 1000 Genomes Browser:

rs553907248

Molecular consequence:

NM_001317186.2:c.-254-2719A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001317184.2:c.1385A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001317185.2:c.20A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.1568A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Rattus norvegicus PKCd gene encoding protein kinase C delta, exon 8
Rattus norvegicus PKCd gene encoding protein kinase C delta, exon 8
gi|7007352|emb|AJ230622.1|

Nucleotide
Rattus norvegicus PKCd gene encoding protein kinase C delta, exon 1 and joined m...
Rattus norvegicus PKCd gene encoding protein kinase C delta, exon 1 and joined mRNA
gi|7019598|emb|AJ230615.1|

Nucleotide
Rattus norvegicus PKCd gene encoding protein kinase C delta, exon 13
Rattus norvegicus PKCd gene encoding protein kinase C delta, exon 13
gi|7007357|emb|AJ230627.1|

Nucleotide
IL1RN interleukin 1 receptor antagonist [Macaca mulatta]
IL1RN interleukin 1 receptor antagonist [Macaca mulatta]
Gene ID:701658

Gene
Neisseria meningitidis strain N753_00 NODE_154_length_639_cov_404.73_ID_307, who...
Neisseria meningitidis strain N753_00 NODE_154_length_639_cov_404.73_ID_307, whole genome shotgun sequence
gi|1269813835|gb|PDVQ01000154.1||gn :PDVQ01|NODE_154_length_639_cov_404.73_ID_307

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000210916	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Dec 11, 2020)	germline	clinical testing	Citation Link,
SCV000600961	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely benign (Feb 6, 2023)	unknown	clinical testing	PubMed (5) [See all records that cite these PMIDs] 29522266, 31780696, 32936981, 27392081, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000210916

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Dec 11, 2020)

germline

clinical testing

Citation Link,

SCV000600961

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Likely benign
(Feb 6, 2023)

unknown

clinical testing

PubMed (5)
[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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Gene panel testing of 5589 BRCA1/2-negative index patients with breast cancer in a routine diagnostic setting: results of the German Consortium for Hereditary Breast and Ovarian Cancer.

Hauke J, Horvath J, Groß E, Gehrig A, Honisch E, Hackmann K, Schmidt G, Arnold N, Faust U, Sutter C, Hentschel J, Wang-Gohrke S, Smogavec M, Weber BHF, Weber-Lassalle N, Weber-Lassalle K, Borde J, Ernst C, Altmüller J, Volk AE, Thiele H, Hübbel V, et al.

Cancer Med. 2018 Apr;7(4):1349-1358. doi: 10.1002/cam4.1376. Epub 2018 Mar 9.

PubMed [citation]

PMID:: 29522266
PMCID:: PMC5911592

Germline variants in cancer genes in high-risk non-BRCA patients from Puerto Rico.

Dutil J, Teer JK, Golubeva V, Yoder S, Tong WL, Arroyo N, Karam R, Echenique M, Matta JL, Monteiro AN.

Sci Rep. 2019 Nov 28;9(1):17769. doi: 10.1038/s41598-019-54170-6.

PubMed [citation]

PMID:: 31780696
PMCID:: PMC6882826

See all PubMed Citations (5)

Details of each submission

From GeneDx, SCV000210916.13

#	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 (Hauke 2018, Dutil 2019); 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: 27181684, 29522266, 31780696, 32936981)

#	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, SCV000600961.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

#	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: Oct 13, 2024

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