NM_000038.6(APC):c.7088A>G (p.Lys2363Arg) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 23, 2015
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:: RCV000115119.11

Allele description [Variation Report for NM_000038.6(APC):c.7088A>G (p.Lys2363Arg)]

NM_000038.6(APC):c.7088A>G (p.Lys2363Arg)

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.7088A>G (p.Lys2363Arg)

Other names:

p.K2363R:AAA>AGA

HGVS:

NC_000005.10:g.112842682A>G
NG_008481.4:g.155162A>G
NM_000038.6:c.7088A>GMANE SELECT
NM_001127510.3:c.7088A>G
NM_001127511.3:c.7034A>G
NM_001354895.2:c.7088A>G
NM_001354896.2:c.7142A>G
NM_001354897.2:c.7118A>G
NM_001354898.2:c.7013A>G
NM_001354899.2:c.7004A>G
NM_001354900.2:c.6965A>G
NM_001354901.2:c.6911A>G
NM_001354902.2:c.6815A>G
NM_001354903.2:c.6785A>G
NM_001354904.2:c.6710A>G
NM_001354905.2:c.6608A>G
NM_001354906.2:c.6239A>G
NP_000029.2:p.Lys2363Arg
NP_001120982.1:p.Lys2363Arg
NP_001120983.2:p.Lys2345Arg
NP_001341824.1:p.Lys2363Arg
NP_001341825.1:p.Lys2381Arg
NP_001341826.1:p.Lys2373Arg
NP_001341827.1:p.Lys2338Arg
NP_001341828.1:p.Lys2335Arg
NP_001341829.1:p.Lys2322Arg
NP_001341830.1:p.Lys2304Arg
NP_001341831.1:p.Lys2272Arg
NP_001341832.1:p.Lys2262Arg
NP_001341833.1:p.Lys2237Arg
NP_001341834.1:p.Lys2203Arg
NP_001341835.1:p.Lys2080Arg
LRG_130:g.155162A>G
NC_000005.9:g.112178379A>G
NM_000038.5:c.7088A>G

Protein change:

K2080R

Links:

dbSNP: rs587779806

NCBI 1000 Genomes Browser:

rs587779806

Molecular consequence:

NM_000038.6:c.7088A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7088A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7034A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7088A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7142A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7118A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7013A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7004A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.6965A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.6911A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.6815A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.6785A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.6710A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.6608A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6239A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000149028	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Jun 23, 2015)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000149028

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Jun 23, 2015)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000149028.14

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

Description

This variant is denoted APC c.7088A>G at the cDNA level, p.Lys2363Arg (K2363R) at the protein level, and results in the change of a Lysine to an Arginine (AAA>AGA). This variant has not, to our knowledge, been published in the literature as pathogenic or benign. APC Lys2363Arg was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Since Lysine and Arginine share similar properties, this is considered a conservative amino acid substitution. APC Lys2363Arg occurs at a position where amino acids with properties similar to Lysine are tolerated across species and is located in the basic domain and the Ser-rich region (Azzopardi 2008, UniProt) In silico analyses are inconsistent regarding the effect this variant may have on protein structure and function. Based on currently available information, it is unclear whether APC Lys2363Arg is pathogenic or benign. We consider it to be a variant of uncertain significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 26, 2024

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