NM_000038.6(APC):c.7809A>C (p.Glu2603Asp) AND Familial adenomatous polyposis 1

delete

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 2, 2022
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:: RCV003653372.1

Allele description

NM_000038.6(APC):c.7809A>C (p.Glu2603Asp)

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.7809A>C (p.Glu2603Asp)

HGVS:

NC_000005.10:g.112843403A>C
NG_008481.4:g.155883A>C
NM_000038.6:c.7809A>CMANE SELECT
NM_001127510.3:c.7809A>C
NM_001127511.3:c.7755A>C
NM_001354895.2:c.7809A>C
NM_001354896.2:c.7863A>C
NM_001354897.2:c.7839A>C
NM_001354898.2:c.7734A>C
NM_001354899.2:c.7725A>C
NM_001354900.2:c.7686A>C
NM_001354901.2:c.7632A>C
NM_001354902.2:c.7536A>C
NM_001354903.2:c.7506A>C
NM_001354904.2:c.7431A>C
NM_001354905.2:c.7329A>C
NM_001354906.2:c.6960A>C
NP_000029.2:p.Glu2603Asp
NP_001120982.1:p.Glu2603Asp
NP_001120983.2:p.Glu2585Asp
NP_001341824.1:p.Glu2603Asp
NP_001341825.1:p.Glu2621Asp
NP_001341826.1:p.Glu2613Asp
NP_001341827.1:p.Glu2578Asp
NP_001341828.1:p.Glu2575Asp
NP_001341829.1:p.Glu2562Asp
NP_001341830.1:p.Glu2544Asp
NP_001341831.1:p.Glu2512Asp
NP_001341832.1:p.Glu2502Asp
NP_001341833.1:p.Glu2477Asp
NP_001341834.1:p.Glu2443Asp
NP_001341835.1:p.Glu2320Asp
LRG_130:g.155883A>C
NC_000005.9:g.112179100A>C
NM_000038.5:c.7809A>C

Protein change:

E2320D

Links:

dbSNP: rs1580686817

NCBI 1000 Genomes Browser:

rs1580686817

Molecular consequence:

NM_000038.6:c.7809A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7809A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7755A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7809A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7863A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7839A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7734A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7725A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.7686A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.7632A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.7536A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.7506A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.7431A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.7329A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6960A>C - missense variant - [Sequence Ontology: SO:0001583]

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
SCV000950088	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 2, 2022)	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

SCV000950088

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 2, 2022)

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, SCV000950088.4

#	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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 654022). This variant has not been reported in the literature in individuals affected with APC-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 2603 of the APC protein (p.Glu2603Asp).

#	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

ClinVar

Relating variation to medicine