NM_000038.6(APC):c.7707T>G (p.Ser2569Arg) AND Familial adenomatous polyposis 1

delete

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 31, 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:: RCV003534640.1

Allele description

NM_000038.6(APC):c.7707T>G (p.Ser2569Arg)

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.7707T>G (p.Ser2569Arg)

HGVS:

NC_000005.10:g.112843301T>G
NG_008481.4:g.155781T>G
NM_000038.6:c.7707T>GMANE SELECT
NM_001127510.3:c.7707T>G
NM_001127511.3:c.7653T>G
NM_001354895.2:c.7707T>G
NM_001354896.2:c.7761T>G
NM_001354897.2:c.7737T>G
NM_001354898.2:c.7632T>G
NM_001354899.2:c.7623T>G
NM_001354900.2:c.7584T>G
NM_001354901.2:c.7530T>G
NM_001354902.2:c.7434T>G
NM_001354903.2:c.7404T>G
NM_001354904.2:c.7329T>G
NM_001354905.2:c.7227T>G
NM_001354906.2:c.6858T>G
NP_000029.2:p.Ser2569Arg
NP_001120982.1:p.Ser2569Arg
NP_001120983.2:p.Ser2551Arg
NP_001341824.1:p.Ser2569Arg
NP_001341825.1:p.Ser2587Arg
NP_001341826.1:p.Ser2579Arg
NP_001341827.1:p.Ser2544Arg
NP_001341828.1:p.Ser2541Arg
NP_001341829.1:p.Ser2528Arg
NP_001341830.1:p.Ser2510Arg
NP_001341831.1:p.Ser2478Arg
NP_001341832.1:p.Ser2468Arg
NP_001341833.1:p.Ser2443Arg
NP_001341834.1:p.Ser2409Arg
NP_001341835.1:p.Ser2286Arg
LRG_130:g.155781T>G
NC_000005.9:g.112178998T>G
NM_000038.5:c.7707T>G

Protein change:

S2286R

Links:

dbSNP: rs985452718

NCBI 1000 Genomes Browser:

rs985452718

Molecular consequence:

NM_000038.6:c.7707T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7707T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7653T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7707T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7761T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7737T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7632T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7623T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.7584T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.7530T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.7434T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.7404T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.7329T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.7227T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6858T>G - 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

Recent activity

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tetraspanin-14 [Mus musculus]
tetraspanin-14 [Mus musculus]
gi|22122345|ref|NP_666040.1|

Protein
diphthine--ammonia ligase isoform 2 [Homo sapiens]
diphthine--ammonia ligase isoform 2 [Homo sapiens]
gi|213972615|ref|NP_001135444.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000823937	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 31, 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

SCV000823937

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 31, 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, SCV000823937.4

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

Description

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. This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 2569 of the APC protein (p.Ser2569Arg). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with APC-related conditions. ClinVar contains an entry for this variant (Variation ID: 573707). 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: Jun 2, 2024

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Relating variation to medicine