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NM_000038.6(APC):c.1809del (p.Ala604fs) AND Familial adenomatous polyposis 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 3, 2019
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:
RCV002553909.10

Allele description [Variation Report for NM_000038.6(APC):c.1809del (p.Ala604fs)]

NM_000038.6(APC):c.1809del (p.Ala604fs)

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.1809del (p.Ala604fs)
HGVS:
  • NC_000005.10:g.112835016del
  • NG_008481.4:g.147496del
  • NM_000038.6:c.1809delMANE SELECT
  • NM_001127510.3:c.1809del
  • NM_001127511.3:c.1755del
  • NM_001354895.2:c.1809del
  • NM_001354896.2:c.1863del
  • NM_001354897.2:c.1839del
  • NM_001354898.2:c.1734del
  • NM_001354899.2:c.1725del
  • NM_001354900.2:c.1686del
  • NM_001354901.2:c.1632del
  • NM_001354902.2:c.1536del
  • NM_001354903.2:c.1506del
  • NM_001354904.2:c.1431del
  • NM_001354905.2:c.1329del
  • NM_001354906.2:c.960del
  • NP_000029.2:p.Ala604fs
  • NP_001120982.1:p.Ala604fs
  • NP_001120983.2:p.Ala586fs
  • NP_001341824.1:p.Ala604fs
  • NP_001341825.1:p.Ala622fs
  • NP_001341826.1:p.Ala614fs
  • NP_001341827.1:p.Ala579fs
  • NP_001341828.1:p.Ala576fs
  • NP_001341829.1:p.Ala563fs
  • NP_001341830.1:p.Ala545fs
  • NP_001341831.1:p.Ala513fs
  • NP_001341832.1:p.Ala503fs
  • NP_001341833.1:p.Ala478fs
  • NP_001341834.1:p.Ala444fs
  • NP_001341835.1:p.Ala321fs
  • LRG_130:g.147496del
  • NC_000005.9:g.112170711del
  • NC_000005.9:g.112170713del
  • NM_000038.5:c.1809del
Protein change:
A321fs
Links:
dbSNP: rs1764704274
NCBI 1000 Genomes Browser:
rs1764704274
Molecular consequence:
  • NM_000038.6:c.1809del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001127510.3:c.1809del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001127511.3:c.1755del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354895.2:c.1809del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354896.2:c.1863del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354897.2:c.1839del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354898.2:c.1734del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354899.2:c.1725del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354900.2:c.1686del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354901.2:c.1632del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354902.2:c.1536del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354903.2:c.1506del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354904.2:c.1431del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354905.2:c.1329del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001354906.2:c.960del - 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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001226721Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 3, 2019) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001226721.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with APC-related conditions. This sequence change creates a premature translational stop signal (p.Ala604Leufs*6) in the APC gene. It is expected to result in an absent or disrupted protein product. For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in APC are known to be pathogenic (PMID: 17963004, 20685668).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024