NM_004360.5(CDH1):c.144_151dup (p.Val51fs) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 10, 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:: RCV003170899.2

Allele description [Variation Report for NM_004360.5(CDH1):c.144_151dup (p.Val51fs)]

NM_004360.5(CDH1):c.144_151dup (p.Val51fs)

Gene:

CDH1:cadherin 1 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

16q22.1

Genomic location:

Preferred name:

NM_004360.5(CDH1):c.144_151dup (p.Val51fs)

HGVS:

NC_000016.10:g.68738392_68738399dup
NG_008021.1:g.6101_6108dup
NM_001317184.2:c.144_151dup
NM_001317185.2:c.-1472_-1465dup
NM_001317186.2:c.-1676_-1669dup
NM_004360.5:c.144_151dupMANE SELECT
NP_001304113.1:p.Val51fs
NP_004351.1:p.Val51Glufs
NP_004351.1:p.Val51fs
LRG_301t1:c.144_151dup
LRG_301:g.6101_6108dup
LRG_301p1:p.Val51Glufs
NC_000016.9:g.68772293_68772294insGAGGCCGC
NC_000016.9:g.68772295_68772302dup
NM_004360.3:c.144_151dup
NM_004360.3:c.144_151dupAGGCCGCG

Protein change:

V51fs

Molecular consequence:

NM_001317185.2:c.-1472_-1465dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317186.2:c.-1676_-1669dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317184.2:c.144_151dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_004360.5:c.144_151dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

Recent activity

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S-phase kinase-associated protein 2 isoform a [Mus musculus]
S-phase kinase-associated protein 2 isoform a [Mus musculus]
gi|7949135|ref|NP_038815.1|

Protein
RecName: Full=Dual specificity mitogen-activated protein kinase kinase 3; Short=...
RecName: Full=Dual specificity mitogen-activated protein kinase kinase 3; Short=MAP kinase kinase 3; Short=MAPKK 3; AltName: Full=MAPK/ERK kinase 3; Short=MEK 3; AltName: Full=Stress-activated protein kinase kinase 2; Short=SAPK kinase 2; Short=SAPKK-2; Short=SAPKK2
gi|24638466|sp|P46734.2|MP2K3_HUMAN

Protein
Pld2 phospholipase D2 [Rattus norvegicus]
Pld2 phospholipase D2 [Rattus norvegicus]
Gene ID:25097

Gene
25097[uid] AND (alive[prop]) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003867771	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Mar 10, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003867771

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Mar 10, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Ambry Genetics, SCV003867771.2

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

Description

The c.144_151dupAGGCCGCG pathogenic mutation, located in coding exon 2 of the CDH1 gene, results from a duplication of AGGCCGCG at nucleotide position 144, causing a translational frameshift with a predicted alternate stop codon (p.V51Efs*8). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

#	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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