NM_000038.6(APC):c.7697G>T (p.Arg2566Ile) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 19, 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:: RCV002400545.2

Allele description [Variation Report for NM_000038.6(APC):c.7697G>T (p.Arg2566Ile)]

NM_000038.6(APC):c.7697G>T (p.Arg2566Ile)

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.7697G>T (p.Arg2566Ile)

HGVS:

NC_000005.10:g.112843291G>T
NG_008481.4:g.155771G>T
NM_000038.6:c.7697G>TMANE SELECT
NM_001127510.3:c.7697G>T
NM_001127511.3:c.7643G>T
NM_001354895.2:c.7697G>T
NM_001354896.2:c.7751G>T
NM_001354897.2:c.7727G>T
NM_001354898.2:c.7622G>T
NM_001354899.2:c.7613G>T
NM_001354900.2:c.7574G>T
NM_001354901.2:c.7520G>T
NM_001354902.2:c.7424G>T
NM_001354903.2:c.7394G>T
NM_001354904.2:c.7319G>T
NM_001354905.2:c.7217G>T
NM_001354906.2:c.6848G>T
NM_001407446.1:c.7781G>T
NM_001407447.1:c.7751G>T
NM_001407448.1:c.7751G>T
NM_001407449.1:c.7751G>T
NM_001407450.1:c.7697G>T
NM_001407451.1:c.7676G>T
NM_001407452.1:c.7667G>T
NM_001407453.1:c.7520G>T
NM_001407454.1:c.7448G>T
NM_001407455.1:c.7448G>T
NM_001407456.1:c.7448G>T
NM_001407457.1:c.7448G>T
NM_001407458.1:c.7394G>T
NM_001407459.1:c.7394G>T
NM_001407460.1:c.7394G>T
NM_001407467.1:c.7310G>T
NM_001407469.1:c.7310G>T
NM_001407470.1:c.6848G>T
NM_001407471.1:c.6545G>T
NM_001407472.1:c.6545G>T
NP_000029.2:p.Arg2566Ile
NP_000029.2:p.Arg2566Ile
NP_001120982.1:p.Arg2566Ile
NP_001120982.1:p.Arg2566Ile
NP_001120983.1:p.Arg2566Ile
NP_001120983.2:p.Arg2548Ile
NP_001341824.1:p.Arg2566Ile
NP_001341825.1:p.Arg2584Ile
NP_001341826.1:p.Arg2576Ile
NP_001341827.1:p.Arg2541Ile
NP_001341828.1:p.Arg2538Ile
NP_001341829.1:p.Arg2525Ile
NP_001341830.1:p.Arg2507Ile
NP_001341831.1:p.Arg2475Ile
NP_001341832.1:p.Arg2465Ile
NP_001341833.1:p.Arg2440Ile
NP_001341834.1:p.Arg2406Ile
NP_001341835.1:p.Arg2283Ile
NP_001394375.1:p.Arg2594Ile
NP_001394376.1:p.Arg2584Ile
NP_001394377.1:p.Arg2584Ile
NP_001394378.1:p.Arg2584Ile
NP_001394379.1:p.Arg2566Ile
NP_001394380.1:p.Arg2559Ile
NP_001394381.1:p.Arg2556Ile
NP_001394382.1:p.Arg2507Ile
NP_001394383.1:p.Arg2483Ile
NP_001394384.1:p.Arg2483Ile
NP_001394385.1:p.Arg2483Ile
NP_001394386.1:p.Arg2483Ile
NP_001394387.1:p.Arg2465Ile
NP_001394388.1:p.Arg2465Ile
NP_001394389.1:p.Arg2465Ile
NP_001394396.1:p.Arg2437Ile
NP_001394398.1:p.Arg2437Ile
NP_001394399.1:p.Arg2283Ile
NP_001394400.1:p.Arg2182Ile
NP_001394401.1:p.Arg2182Ile
LRG_130t1:c.7697G>T
LRG_130t2:c.7697G>T
LRG_130t3:c.7697G>T
LRG_130:g.155771G>T
LRG_130p1:p.Arg2566Ile
LRG_130p2:p.Arg2566Ile
LRG_130p3:p.Arg2566Ile
NC_000005.9:g.112178988G>T
NM_000038.4:c.7697G>T
NM_000038.5:c.7697G>T
NM_001127510.1:c.7697G>T
NM_001127511.1:c.7697G>T
NR_176365.1:n.7532G>T
NR_176366.1:n.7951G>T

Protein change:

R2182I

Molecular consequence:

NM_000038.6:c.7697G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7697G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7643G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7697G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7751G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7727G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7622G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7613G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.7574G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.7520G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.7424G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.7394G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.7319G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.7217G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6848G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407446.1:c.7781G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407447.1:c.7751G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407448.1:c.7751G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407449.1:c.7751G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407450.1:c.7697G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407451.1:c.7676G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407452.1:c.7667G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407453.1:c.7520G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407454.1:c.7448G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407455.1:c.7448G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407456.1:c.7448G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407457.1:c.7448G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407458.1:c.7394G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407459.1:c.7394G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407460.1:c.7394G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407467.1:c.7310G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407469.1:c.7310G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407470.1:c.6848G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407471.1:c.6545G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407472.1:c.6545G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

Recent activity

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CUGBP Elav-like family member 4 isoform 16 [Mus musculus]
CUGBP Elav-like family member 4 isoform 16 [Mus musculus]
gi|1376476229|ref|NP_001349220.1|

Protein
txid7955[organism] AND (aldh16a1[gene symbol] OR (BC129186 OR BC1... (18)
txid7955[organism] AND (aldh16a1[gene symbol] OR (BC129186 OR BC129186.* OR CK688419 OR CK688419.* OR GFIL01000851 OR GFIL01000851.* OR BC129186 OR BC129186.* OR BC091851 OR BC091851.* OR XM_005164021 OR XM_005164021.* OR NM_001079954 OR NM_001079954.*))
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GEO Profiles
RING/U-box superfamily protein [Arabidopsis thaliana]
RING/U-box superfamily protein [Arabidopsis thaliana]
Gene ID:836739

Gene
836739[uid] AND (alive[prop]) (1)
Gene
PREDICTED: LOB domain-containing protein 25-like isoform X1 [Nicotiana sylvestri...
PREDICTED: LOB domain-containing protein 25-like isoform X1 [Nicotiana sylvestris]
gi|698522132|ref|XP_009757880.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002669517	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jan 19, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002669517

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jan 19, 2022)

germline

clinical testing

Citation Link

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

Details of each submission

From Ambry Genetics, SCV002669517.2

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

Description

The p.R2566I variant (also known as c.7697G>T), located in coding exon 15 of the APC gene, results from a G to T substitution at nucleotide position 7697. The arginine at codon 2566 is replaced by isoleucine, an amino acid with similar properties. This amino acid position is conserved. In addition, in silico predictors for this gene do not accurately predict pathogenicity. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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: May 1, 2024

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