NM_000038.6(APC):c.7828G>A (p.Gly2610Arg) AND Familial adenomatous polyposis 1

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Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 17, 2021
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:: RCV003744913.1

Allele description

NM_000038.6(APC):c.7828G>A (p.Gly2610Arg)

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.7828G>A (p.Gly2610Arg)

HGVS:

NC_000005.10:g.112843422G>A
NG_008481.4:g.155902G>A
NM_000038.5:c.7828G>A
NM_000038.6:c.7828G>AMANE SELECT
NM_001127510.3:c.7828G>A
NM_001127511.3:c.7774G>A
NM_001354895.2:c.7828G>A
NM_001354896.2:c.7882G>A
NM_001354897.2:c.7858G>A
NM_001354898.2:c.7753G>A
NM_001354899.2:c.7744G>A
NM_001354900.2:c.7705G>A
NM_001354901.2:c.7651G>A
NM_001354902.2:c.7555G>A
NM_001354903.2:c.7525G>A
NM_001354904.2:c.7450G>A
NM_001354905.2:c.7348G>A
NM_001354906.2:c.6979G>A
NM_001407446.1:c.7912G>A
NM_001407447.1:c.7882G>A
NM_001407448.1:c.7882G>A
NM_001407449.1:c.7882G>A
NM_001407450.1:c.7828G>A
NM_001407451.1:c.7807G>A
NM_001407452.1:c.7798G>A
NM_001407453.1:c.7651G>A
NM_001407454.1:c.7579G>A
NM_001407455.1:c.7579G>A
NM_001407456.1:c.7579G>A
NM_001407457.1:c.7579G>A
NM_001407458.1:c.7525G>A
NM_001407459.1:c.7525G>A
NM_001407460.1:c.7525G>A
NM_001407467.1:c.7441G>A
NM_001407469.1:c.7441G>A
NM_001407470.1:c.6979G>A
NM_001407471.1:c.6676G>A
NM_001407472.1:c.6676G>A
NP_000029.2:p.Gly2610Arg
NP_000029.2:p.Gly2610Arg
NP_001120982.1:p.Gly2610Arg
NP_001120982.1:p.Gly2610Arg
NP_001120983.1:p.Gly2610Arg
NP_001120983.2:p.Gly2592Arg
NP_001341824.1:p.Gly2610Arg
NP_001341825.1:p.Gly2628Arg
NP_001341826.1:p.Gly2620Arg
NP_001341827.1:p.Gly2585Arg
NP_001341828.1:p.Gly2582Arg
NP_001341829.1:p.Gly2569Arg
NP_001341830.1:p.Gly2551Arg
NP_001341831.1:p.Gly2519Arg
NP_001341832.1:p.Gly2509Arg
NP_001341833.1:p.Gly2484Arg
NP_001341834.1:p.Gly2450Arg
NP_001341835.1:p.Gly2327Arg
NP_001394375.1:p.Gly2638Arg
NP_001394376.1:p.Gly2628Arg
NP_001394377.1:p.Gly2628Arg
NP_001394378.1:p.Gly2628Arg
NP_001394379.1:p.Gly2610Arg
NP_001394380.1:p.Gly2603Arg
NP_001394381.1:p.Gly2600Arg
NP_001394382.1:p.Gly2551Arg
NP_001394383.1:p.Gly2527Arg
NP_001394384.1:p.Gly2527Arg
NP_001394385.1:p.Gly2527Arg
NP_001394386.1:p.Gly2527Arg
NP_001394387.1:p.Gly2509Arg
NP_001394388.1:p.Gly2509Arg
NP_001394389.1:p.Gly2509Arg
NP_001394396.1:p.Gly2481Arg
NP_001394398.1:p.Gly2481Arg
NP_001394399.1:p.Gly2327Arg
NP_001394400.1:p.Gly2226Arg
NP_001394401.1:p.Gly2226Arg
LRG_130t1:c.7828G>A
LRG_130t2:c.7828G>A
LRG_130t3:c.7828G>A
LRG_130:g.155902G>A
LRG_130p1:p.Gly2610Arg
LRG_130p2:p.Gly2610Arg
LRG_130p3:p.Gly2610Arg
NC_000005.9:g.112179119G>A
NM_000038.4:c.7828G>A
NM_001127510.1:c.7828G>A
NM_001127511.1:c.7828G>A
NR_176365.1:n.7663G>A
NR_176366.1:n.8082G>A

Protein change:

G2226R

Molecular consequence:

NM_000038.6:c.7828G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7828G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7774G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7828G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7882G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7858G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7753G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7744G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.7705G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.7651G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.7555G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.7525G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.7450G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.7348G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6979G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407446.1:c.7912G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407447.1:c.7882G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407448.1:c.7882G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407449.1:c.7882G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407450.1:c.7828G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407451.1:c.7807G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407452.1:c.7798G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407453.1:c.7651G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407454.1:c.7579G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407455.1:c.7579G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407456.1:c.7579G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407457.1:c.7579G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407458.1:c.7525G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407459.1:c.7525G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407460.1:c.7525G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407467.1:c.7441G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407469.1:c.7441G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407470.1:c.6979G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407471.1:c.6676G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001407472.1:c.6676G>A - 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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paraneoplastic antigen Ma1 homolog [Mus musculus]
paraneoplastic antigen Ma1 homolog [Mus musculus]
gi|148287013|ref|NP_081714.2|

Protein
Sertm1 serine rich and transmembrane domain containing 1 [Mus musculus]
Sertm1 serine rich and transmembrane domain containing 1 [Mus musculus]
Gene ID:329641

Gene
329641[uid] AND (alive[prop]) (1)
Gene
Profile neighbors for GEO Profiles (Select 6124914) (199)
GEO Profiles
PMC Links for GEO Profiles (Select 34520996) (17)
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003322943	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 17, 2021)	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

SCV003322943

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 17, 2021)

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, SCV003322943.2

#	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 (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. 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 glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 2610 of the APC protein (p.Gly2610Arg).

#	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 9, 2024

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