NM_004360.5(CDH1):c.1566A>G (p.Thr522=) AND Hereditary diffuse gastric adenocarcinoma

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 11, 2017
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:: RCV000556484.5

Allele description [Variation Report for NM_004360.5(CDH1):c.1566A>G (p.Thr522=)]

NM_004360.5(CDH1):c.1566A>G (p.Thr522=)

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.1566A>G (p.Thr522=)

HGVS:

NC_000016.10:g.68819280A>G
NG_008021.1:g.86989A>G
NM_001317184.2:c.1383A>G
NM_001317185.2:c.18A>G
NM_001317186.2:c.-254-2721A>G
NM_004360.5:c.1566A>GMANE SELECT
NP_001304113.1:p.Thr461=
NP_001304114.1:p.Thr6=
NP_004351.1:p.Thr522=
LRG_301t1:c.1566A>G
LRG_301:g.86989A>G
NC_000016.9:g.68853183A>G
NM_004360.3:c.1566A>G
NM_004360.4:c.1566A>G

Links:

dbSNP: rs1555516521

NCBI 1000 Genomes Browser:

rs1555516521

Molecular consequence:

NM_001317186.2:c.-254-2721A>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001317184.2:c.1383A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001317185.2:c.18A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_004360.5:c.1566A>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Hereditary diffuse gastric adenocarcinoma (HDGC)
Synonyms:: Hereditary diffuse gastric cancer
Identifiers:: MONDO: MONDO:0007648; MedGen: C1708349; Orphanet: 26106; OMIM: 137215

Recent activity

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Homo sapiens apolipoprotein C4 (APOC4), mRNA
Homo sapiens apolipoprotein C4 (APOC4), mRNA
gi|1519312222|ref|NM_001646.3|

Nucleotide
Selaginella jugorum voucher Zuo Z.Y. zuo2325 (KUN) 26S large subunit ribosomal R...
Selaginella jugorum voucher Zuo Z.Y. zuo2325 (KUN) 26S large subunit ribosomal RNA gene, partial sequence
gi|2431446218|gb|ON098442.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000637735	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 11, 2017)	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

SCV000637735

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 11, 2017)

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000637735.4

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

Description

This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a CDH1-related disease. In summary, this is a novel silent change with uncertain impact on splicing. It has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may alter RNA splicing, but this prediction has not been confirmed by published transcriptional studies. This sequence change affects codon522 of the CDH1 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the CDH1 protein.

#	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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