NM_000038.6(APC):c.7789G>A (p.Gly2597Arg) AND Familial adenomatous polyposis 1

delete

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 1, 2023
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:: RCV003652405.1

Allele description

NM_000038.6(APC):c.7789G>A (p.Gly2597Arg)

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.7789G>A (p.Gly2597Arg)

HGVS:

NC_000005.10:g.112843383G>A
NG_008481.4:g.155863G>A
NM_000038.6:c.7789G>AMANE SELECT
NM_001127510.3:c.7789G>A
NM_001127511.3:c.7735G>A
NM_001354895.2:c.7789G>A
NM_001354896.2:c.7843G>A
NM_001354897.2:c.7819G>A
NM_001354898.2:c.7714G>A
NM_001354899.2:c.7705G>A
NM_001354900.2:c.7666G>A
NM_001354901.2:c.7612G>A
NM_001354902.2:c.7516G>A
NM_001354903.2:c.7486G>A
NM_001354904.2:c.7411G>A
NM_001354905.2:c.7309G>A
NM_001354906.2:c.6940G>A
NM_001407446.1:c.7873G>A
NM_001407447.1:c.7843G>A
NM_001407448.1:c.7843G>A
NM_001407449.1:c.7843G>A
NM_001407450.1:c.7789G>A
NM_001407451.1:c.7768G>A
NM_001407452.1:c.7759G>A
NM_001407453.1:c.7612G>A
NM_001407454.1:c.7540G>A
NM_001407455.1:c.7540G>A
NM_001407456.1:c.7540G>A
NM_001407457.1:c.7540G>A
NM_001407458.1:c.7486G>A
NM_001407459.1:c.7486G>A
NM_001407460.1:c.7486G>A
NM_001407467.1:c.7402G>A
NM_001407469.1:c.7402G>A
NM_001407470.1:c.6940G>A
NM_001407471.1:c.6637G>A
NM_001407472.1:c.6637G>A
NP_000029.2:p.Gly2597Arg
NP_000029.2:p.Gly2597Arg
NP_001120982.1:p.Gly2597Arg
NP_001120982.1:p.Gly2597Arg
NP_001120983.1:p.Gly2597Arg
NP_001120983.2:p.Gly2579Arg
NP_001341824.1:p.Gly2597Arg
NP_001341825.1:p.Gly2615Arg
NP_001341826.1:p.Gly2607Arg
NP_001341827.1:p.Gly2572Arg
NP_001341828.1:p.Gly2569Arg
NP_001341829.1:p.Gly2556Arg
NP_001341830.1:p.Gly2538Arg
NP_001341831.1:p.Gly2506Arg
NP_001341832.1:p.Gly2496Arg
NP_001341833.1:p.Gly2471Arg
NP_001341834.1:p.Gly2437Arg
NP_001341835.1:p.Gly2314Arg
NP_001394375.1:p.Gly2625Arg
NP_001394376.1:p.Gly2615Arg
NP_001394377.1:p.Gly2615Arg
NP_001394378.1:p.Gly2615Arg
NP_001394379.1:p.Gly2597Arg
NP_001394380.1:p.Gly2590Arg
NP_001394381.1:p.Gly2587Arg
NP_001394382.1:p.Gly2538Arg
NP_001394383.1:p.Gly2514Arg
NP_001394384.1:p.Gly2514Arg
NP_001394385.1:p.Gly2514Arg
NP_001394386.1:p.Gly2514Arg
NP_001394387.1:p.Gly2496Arg
NP_001394388.1:p.Gly2496Arg
NP_001394389.1:p.Gly2496Arg
NP_001394396.1:p.Gly2468Arg
NP_001394398.1:p.Gly2468Arg
NP_001394399.1:p.Gly2314Arg
NP_001394400.1:p.Gly2213Arg
NP_001394401.1:p.Gly2213Arg
LRG_130t1:c.7789G>A
LRG_130t2:c.7789G>A
LRG_130t3:c.7789G>A
LRG_130:g.155863G>A
LRG_130p1:p.Gly2597Arg
LRG_130p2:p.Gly2597Arg
LRG_130p3:p.Gly2597Arg
NC_000005.9:g.112179080G>A
NM_000038.4:c.7789G>A
NM_001127510.1:c.7789G>A
NM_001127511.1:c.7789G>A
NR_176365.1:n.7624G>A
NR_176366.1:n.8043G>A

Protein change:

G2213R

Molecular consequence:

NM_000038.6:c.7789G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7789G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7735G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7789G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7843G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7819G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7714G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7705G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.7666G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.7612G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.7516G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.7486G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.7411G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.7309G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6940G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407446.1:c.7873G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407447.1:c.7843G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407448.1:c.7843G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407449.1:c.7843G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407450.1:c.7789G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407451.1:c.7768G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407452.1:c.7759G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407453.1:c.7612G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407454.1:c.7540G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407455.1:c.7540G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407456.1:c.7540G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407457.1:c.7540G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407458.1:c.7486G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407459.1:c.7486G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407460.1:c.7486G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407467.1:c.7402G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407469.1:c.7402G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407470.1:c.6940G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407471.1:c.6637G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407472.1:c.6637G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_176365.1:n.7624G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176366.1:n.8043G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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
SCV004502092	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 1, 2023)	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

SCV004502092

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 1, 2023)

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, SCV004502092.1

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

Description

This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 2597 of the APC protein (p.Gly2597Arg). This variant has not been reported in the literature in individuals affected with APC-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt APC protein function. 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.

#	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: Feb 28, 2024

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