NM_004360.5(CDH1):c.88C>A (p.Pro30Thr) AND Hereditary cancer-predisposing syndrome

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Oct 22, 2020
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:: RCV000115864.16

Allele description [Variation Report for NM_004360.5(CDH1):c.88C>A (p.Pro30Thr)]

NM_004360.5(CDH1):c.88C>A (p.Pro30Thr)

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.88C>A (p.Pro30Thr)

Other names:

p.P30T:CCT>ACT; NM_004360.4(CDH1):c.88C>A

HGVS:

NC_000016.10:g.68738336C>A
NG_008021.1:g.6045C>A
NM_001317184.2:c.88C>A
NM_001317185.2:c.-1528C>A
NM_001317186.2:c.-1732C>A
NM_004360.5:c.88C>AMANE SELECT
NP_001304113.1:p.Pro30Thr
NP_004351.1:p.Pro30Thr
LRG_301t1:c.88C>A
LRG_301:g.6045C>A
NC_000016.9:g.68772239C>A
NM_004360.3:c.88C>A
NM_004360.4:c.88C>A
p.P30T

Protein change:

P30T

Links:

dbSNP: rs139866691

NCBI 1000 Genomes Browser:

rs139866691

Molecular consequence:

NM_001317185.2:c.-1528C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317186.2:c.-1732C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001317184.2:c.88C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004360.5:c.88C>A - missense variant - [Sequence Ontology: SO:0001583]

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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alpha-lactalbumin precursor [Sus scrofa]
alpha-lactalbumin precursor [Sus scrofa]
gi|47523778|ref|NP_999525.1|

Protein
SWAP70 switching B cell complex subunit SWAP70 [Homo sapiens]
SWAP70 switching B cell complex subunit SWAP70 [Homo sapiens]
Gene ID:23075

Gene
23075[uid] AND (alive[prop]) (1)
Gene
RecName: Full=Protein polybromo-1; Short=hPB1; AltName: Full=BRG1-associated fac...
RecName: Full=Protein polybromo-1; Short=hPB1; AltName: Full=BRG1-associated factor 180; Short=BAF180; AltName: Full=Polybromo-1D
gi|73921624|sp|Q86U86.1|PB1_HUMAN

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000172834	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Benign (Aug 7, 2014)	germline	clinical testing	Citation Link,
SCV000537410	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Oct 27, 2015)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000787986	True Health Diagnostics	no assertion criteria provided	Likely benign (Jul 17, 2017)	germline	clinical testing
SCV002529220	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Benign (Oct 22, 2020)	germline	curation	Citation Link

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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, curation

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Ambry Genetics, SCV000172834.9

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

Description

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

#	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

From Color Diagnostics, LLC DBA Color Health, SCV000537410.1

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

#	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

From True Health Diagnostics, SCV000787986.1

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

#	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

From Sema4, Sema4, SCV002529220.1

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

#	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: Oct 20, 2024

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