NM_000038.6(APC):c.1313-2_1743+144del 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:: RCV001358252.1

Allele description [Variation Report for NM_000038.6(APC):c.1313-2_1743+144del]

NM_000038.6(APC):c.1313-2_1743+144del

Gene:

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

Variant type:

Deletion

Cytogenetic location:

5q22.2

Genomic location:

Preferred name:

NM_000038.6(APC):c.1313-2_1743+144del

HGVS:

NC_000005.10:g.112821894_112829116del
NG_008481.4:g.134374_141596del
NM_000038.6:c.1313-2_1743+144delMANE SELECT
NM_001127510.3:c.1313-2_1743+144del
NM_001127511.3:c.1259-2_1689+144del
NM_001354895.2:c.1313-2_1743+144del
NM_001354896.2:c.1313-2_1797+144del
NM_001354897.2:c.1343-2_1773+144del
NM_001354898.2:c.1238-2_1668+144del
NM_001354899.2:c.1229-2_1659+144del
NM_001354900.2:c.1136-2_1620+144del
NM_001354901.2:c.1136-2_1566+144del
NM_001354902.2:c.1040-2_1470+144del
NM_001354903.2:c.1010-2_1440+144del
NM_001354904.2:c.935-2_1365+144del
NM_001354905.2:c.833-2_1263+144del
NM_001354906.2:c.464-2_894+144del
LRG_130:g.134374_141596del
NC_000005.9:g.112157591_112164813del

Molecular consequence:

NM_000038.6:c.1313-2_1743+144del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001127510.3:c.1313-2_1743+144del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001127511.3:c.1259-2_1689+144del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354895.2:c.1313-2_1743+144del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354896.2:c.1313-2_1797+144del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354897.2:c.1343-2_1773+144del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354898.2:c.1238-2_1668+144del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354899.2:c.1229-2_1659+144del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354900.2:c.1136-2_1620+144del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354901.2:c.1136-2_1566+144del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354902.2:c.1040-2_1470+144del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354903.2:c.1010-2_1440+144del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354904.2:c.935-2_1365+144del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354905.2:c.833-2_1263+144del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_001354906.2:c.464-2_894+144del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_000038.6:c.1313-2_1743+144del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001127510.3:c.1313-2_1743+144del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001127511.3:c.1259-2_1689+144del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354895.2:c.1313-2_1743+144del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354896.2:c.1313-2_1797+144del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354897.2:c.1343-2_1773+144del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354898.2:c.1238-2_1668+144del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354899.2:c.1229-2_1659+144del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354900.2:c.1136-2_1620+144del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354901.2:c.1136-2_1566+144del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354902.2:c.1040-2_1470+144del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354903.2:c.1010-2_1440+144del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354904.2:c.935-2_1365+144del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354905.2:c.833-2_1263+144del - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001354906.2:c.464-2_894+144del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

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

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annexin A5 [Mus musculus]
annexin A5 [Mus musculus]
gi|6753060|ref|NP_033803.1|

Protein
Gordonia phage Nymphadora, complete genome
Gordonia phage Nymphadora, complete genome
gi|1012163957|gb|KU963255.1|

Nucleotide
Phellinus laevigatus KCTC 6229 28S ribosomal RNA gene, partial sequence
Phellinus laevigatus KCTC 6229 28S ribosomal RNA gene, partial sequence
gi|18092628|gb|AF458460.1|AF458460

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001553930	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

SCV001553930

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), SCV001553930.1

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

Description

The c.1313-?_8532+?del variant was not identified in the literature. Although the precise breakpoints were not determined, this deletion encompasses the region from exon 13 to exon 18. This type of alteration is predicted to result in a truncated or absent protein and loss of function. Loss of function variants of the APC gene are an established mechanism of disease and is the type of alteration expected to cause familial adenomatous polyposis. In summary, based on the above information, this variant is classified as 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 5, 2022

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