NM_000038.6(APC):c.1370C>A (p.Ser457Ter) AND Carcinoma of colon

Germline classification:: Pathogenic (1 submission)
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV000501164.10

Allele description [Variation Report for NM_000038.6(APC):c.1370C>A (p.Ser457Ter)]

NM_000038.6(APC):c.1370C>A (p.Ser457Ter)

Gene:

APC:APC regulator of WNT signaling pathway [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q22.2

Genomic location:

Preferred name:

NM_000038.6(APC):c.1370C>A (p.Ser457Ter)

HGVS:

NC_000005.10:g.112821953C>A
NG_008481.4:g.134433C>A
NM_000038.6:c.1370C>AMANE SELECT
NM_001127510.3:c.1370C>A
NM_001127511.3:c.1316C>A
NM_001354895.2:c.1370C>A
NM_001354896.2:c.1370C>A
NM_001354897.2:c.1400C>A
NM_001354898.2:c.1295C>A
NM_001354899.2:c.1286C>A
NM_001354900.2:c.1193C>A
NM_001354901.2:c.1193C>A
NM_001354902.2:c.1097C>A
NM_001354903.2:c.1067C>A
NM_001354904.2:c.992C>A
NM_001354905.2:c.890C>A
NM_001354906.2:c.521C>A
NP_000029.2:p.Ser457Ter
NP_001120982.1:p.Ser457Ter
NP_001120983.2:p.Ser439Ter
NP_001341824.1:p.Ser457Ter
NP_001341825.1:p.Ser457Ter
NP_001341826.1:p.Ser467Ter
NP_001341827.1:p.Ser432Ter
NP_001341828.1:p.Ser429Ter
NP_001341829.1:p.Ser398Ter
NP_001341830.1:p.Ser398Ter
NP_001341831.1:p.Ser366Ter
NP_001341832.1:p.Ser356Ter
NP_001341833.1:p.Ser331Ter
NP_001341834.1:p.Ser297Ter
NP_001341835.1:p.Ser174Ter
LRG_130:g.134433C>A
NC_000005.9:g.112157650C>A
NM_000038.5:c.1370C>A
p.Ser457*

Protein change:

S174*

Links:

dbSNP: rs1060503333

NCBI 1000 Genomes Browser:

rs1060503333

Molecular consequence:

NM_000038.6:c.1370C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001127510.3:c.1370C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001127511.3:c.1316C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354895.2:c.1370C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354896.2:c.1370C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354897.2:c.1400C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354898.2:c.1295C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354899.2:c.1286C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354900.2:c.1193C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354901.2:c.1193C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354902.2:c.1097C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354903.2:c.1067C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354904.2:c.992C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354905.2:c.890C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354906.2:c.521C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Carcinoma of colon (CRC)
Synonyms:: Colonic carcinoma; Colon carcinoma
Identifiers:: MONDO: MONDO:0002032; MedGen: C0699790

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000591071	Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR) See additional submitters Franklin by Genoox	no assertion criteria provided	Pathogenic	unknown	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000591071

Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided

Pathogenic

unknown

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV000591071.3

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

Description

The p.Ser457X variant results in a stop codon at postion Ser457 which is predicted to cause premature truncation of the protein product. This is a loss of function DNA variant and loss of function is an established disease mechanism for the APC gene. In addition, this variant has been previously reported in individuals with familial adenomatous polyposis (FAP) (Wallis_1994_7959691, Friedl_2005_20223039, Stekrova_2007_17411426). In summary, based on the above information this variant meets our criteria for being Pathogenic.

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

Last Updated: Nov 10, 2024

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