NM_000038.6(APC):c.1809_1816dup (p.Ile606fs) AND Familial adenomatous polyposis 1

delete

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 24, 2018
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:: RCV003538770.1

Allele description

NM_000038.6(APC):c.1809_1816dup (p.Ile606fs)

Gene:

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

Variant type:

Duplication

Cytogenetic location:

5q22.2

Genomic location:

Preferred name:

NM_000038.6(APC):c.1809_1816dup (p.Ile606fs)

HGVS:

NC_000005.10:g.112835016_112835023dup
NG_008481.4:g.147496_147503dup
NM_000038.6:c.1809_1816dupMANE SELECT
NM_001127510.3:c.1809_1816dup
NM_001127511.3:c.1755_1762dup
NM_001354895.2:c.1809_1816dup
NM_001354896.2:c.1863_1870dup
NM_001354897.2:c.1839_1846dup
NM_001354898.2:c.1734_1741dup
NM_001354899.2:c.1725_1732dup
NM_001354900.2:c.1686_1693dup
NM_001354901.2:c.1632_1639dup
NM_001354902.2:c.1536_1543dup
NM_001354903.2:c.1506_1513dup
NM_001354904.2:c.1431_1438dup
NM_001354905.2:c.1329_1336dup
NM_001354906.2:c.960_967dup
NP_000029.2:p.Ile606fs
NP_001120982.1:p.Ile606fs
NP_001120983.2:p.Ile588fs
NP_001341824.1:p.Ile606fs
NP_001341825.1:p.Ile624fs
NP_001341826.1:p.Ile616fs
NP_001341827.1:p.Ile581fs
NP_001341828.1:p.Ile578fs
NP_001341829.1:p.Ile565fs
NP_001341830.1:p.Ile547fs
NP_001341831.1:p.Ile515fs
NP_001341832.1:p.Ile505fs
NP_001341833.1:p.Ile480fs
NP_001341834.1:p.Ile446fs
NP_001341835.1:p.Ile323fs
LRG_130:g.147496_147503dup
NC_000005.9:g.112170711_112170712insAAGCTGAT
NC_000005.9:g.112170713_112170720dup

Protein change:

I323fs

Links:

dbSNP: rs2149841774

NCBI 1000 Genomes Browser:

rs2149841774

Molecular consequence:

NM_000038.6:c.1809_1816dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001127510.3:c.1809_1816dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001127511.3:c.1755_1762dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354895.2:c.1809_1816dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354896.2:c.1863_1870dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354897.2:c.1839_1846dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354898.2:c.1734_1741dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354899.2:c.1725_1732dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354900.2:c.1686_1693dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354901.2:c.1632_1639dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354902.2:c.1536_1543dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354903.2:c.1506_1513dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354904.2:c.1431_1438dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354905.2:c.1329_1336dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354906.2:c.960_967dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Familial adenomatous polyposis 1 (FAP1)
Synonyms:: POLYPOSIS, ADENOMATOUS INTESTINAL; FAMILIAL ADENOMATOUS POLYPOSIS 1, ATTENUATED; APC-Associated Polyposis Conditions
Identifiers:: MONDO: MONDO:0021056; MedGen: C2713442; OMIM: 175100

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001583709	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 24, 2018)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 17963004, 20685668, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001583709

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 24, 2018)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Mutational screening of the APC gene in Chilean families with familial adenomatous polyposis: nine novel truncating mutations.

De la Fuente MK, Alvarez KP, Letelier AJ, Bellolio F, Acuña ML, León FS, Pinto E, Carvallo P, López-Köstner F.

Dis Colon Rectum. 2007 Dec;50(12):2142-8.

PubMed [citation]

PMID:: 17963004

Germline APC mutation spectrum derived from 863 genomic variations identified through a 15-year medical genetics service to French patients with FAP.

Lagarde A, Rouleau E, Ferrari A, Noguchi T, Qiu J, Briaux A, Bourdon V, Rémy V, Gaildrat P, Adélaïde J, Birnbaum D, Lidereau R, Sobol H, Olschwang S.

J Med Genet. 2010 Oct;47(10):721-2. doi: 10.1136/jmg.2010.078964. Epub 2010 Aug 3.

PubMed [citation]

PMID:: 20685668

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001583709.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in APC are known to be pathogenic (PMID: 17963004, 20685668). This variant has not been reported in the literature in individuals with APC-related disease. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Ile606Lysfs*7) in the APC gene. It is expected to result in an absent or disrupted protein product.

#	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: Jun 2, 2024

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