NM_000038.6(APC):c.8140_8141del (p.Arg2714fs) AND Familial adenomatous polyposis 1

delete

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 18, 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:: RCV003534643.1

Allele description

NM_000038.6(APC):c.8140_8141del (p.Arg2714fs)

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.8140_8141del (p.Arg2714fs)

HGVS:

NC_000005.10:g.112843734_112843735del
NC_000005.9:g.112179430_112179431del
NG_008481.4:g.156214_156215del
NM_000038.6:c.8140_8141delMANE SELECT
NM_001127510.3:c.8140_8141del
NM_001127511.3:c.8086_8087del
NM_001354895.2:c.8140_8141del
NM_001354896.2:c.8194_8195del
NM_001354897.2:c.8170_8171del
NM_001354898.2:c.8065_8066del
NM_001354899.2:c.8056_8057del
NM_001354900.2:c.8017_8018del
NM_001354901.2:c.7963_7964del
NM_001354902.2:c.7867_7868del
NM_001354903.2:c.7837_7838del
NM_001354904.2:c.7762_7763del
NM_001354905.2:c.7660_7661del
NM_001354906.2:c.7291_7292del
NP_000029.2:p.Arg2714fs
NP_001120982.1:p.Arg2714fs
NP_001120983.2:p.Arg2696fs
NP_001341824.1:p.Arg2714fs
NP_001341825.1:p.Arg2732fs
NP_001341826.1:p.Arg2724fs
NP_001341827.1:p.Arg2689fs
NP_001341828.1:p.Arg2686fs
NP_001341829.1:p.Arg2673fs
NP_001341830.1:p.Arg2655fs
NP_001341831.1:p.Arg2623fs
NP_001341832.1:p.Arg2613fs
NP_001341833.1:p.Arg2588fs
NP_001341834.1:p.Arg2554fs
NP_001341835.1:p.Arg2431fs
LRG_130:g.156214_156215del
NC_000005.9:g.112179430_112179431del
NC_000005.9:g.112179430_112179431delGC
NC_000005.9:g.112179431_112179432del
NM_000038.5:c.8140_8141delCG

Protein change:

R2431fs

Links:

dbSNP: rs1561620875

NCBI 1000 Genomes Browser:

rs1561620875

Molecular consequence:

NM_000038.6:c.8140_8141del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001127510.3:c.8140_8141del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001127511.3:c.8086_8087del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354895.2:c.8140_8141del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354896.2:c.8194_8195del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354897.2:c.8170_8171del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354898.2:c.8065_8066del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354899.2:c.8056_8057del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354900.2:c.8017_8018del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354901.2:c.7963_7964del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354902.2:c.7867_7868del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354903.2:c.7837_7838del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354904.2:c.7762_7763del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354905.2:c.7660_7661del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354906.2:c.7291_7292del - 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
SCV000824266	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 18, 2018)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000824266

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 18, 2018)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000824266.4

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. 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 results in a premature translational stop signal in the APC gene (p.Arg2714Tyrfs*18). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 130 amino acids of the APC protein.

#	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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