NM_000038.6(APC):c.7118T>G (p.Met2373Arg) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 22, 2016
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:: RCV000573212.11

Allele description [Variation Report for NM_000038.6(APC):c.7118T>G (p.Met2373Arg)]

NM_000038.6(APC):c.7118T>G (p.Met2373Arg)

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.7118T>G (p.Met2373Arg)

HGVS:

NC_000005.10:g.112842712T>G
NG_008481.4:g.155192T>G
NM_000038.6:c.7118T>GMANE SELECT
NM_001127510.3:c.7118T>G
NM_001127511.3:c.7064T>G
NM_001354895.2:c.7118T>G
NM_001354896.2:c.7172T>G
NM_001354897.2:c.7148T>G
NM_001354898.2:c.7043T>G
NM_001354899.2:c.7034T>G
NM_001354900.2:c.6995T>G
NM_001354901.2:c.6941T>G
NM_001354902.2:c.6845T>G
NM_001354903.2:c.6815T>G
NM_001354904.2:c.6740T>G
NM_001354905.2:c.6638T>G
NM_001354906.2:c.6269T>G
NP_000029.2:p.Met2373Arg
NP_001120982.1:p.Met2373Arg
NP_001120983.2:p.Met2355Arg
NP_001341824.1:p.Met2373Arg
NP_001341825.1:p.Met2391Arg
NP_001341826.1:p.Met2383Arg
NP_001341827.1:p.Met2348Arg
NP_001341828.1:p.Met2345Arg
NP_001341829.1:p.Met2332Arg
NP_001341830.1:p.Met2314Arg
NP_001341831.1:p.Met2282Arg
NP_001341832.1:p.Met2272Arg
NP_001341833.1:p.Met2247Arg
NP_001341834.1:p.Met2213Arg
NP_001341835.1:p.Met2090Arg
LRG_130:g.155192T>G
NC_000005.9:g.112178409T>G
NM_000038.5:c.7118T>G

Protein change:

M2090R

Links:

dbSNP: rs1060503286

NCBI 1000 Genomes Browser:

rs1060503286

Molecular consequence:

NM_000038.6:c.7118T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7118T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7064T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7118T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7172T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7148T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7043T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7034T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.6995T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.6941T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.6845T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.6815T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.6740T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.6638T>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6269T>G - 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

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000675886	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Sep 22, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000675886

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Sep 22, 2016)

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, SCV000675886.5

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

Description

The p.M2373R variant (also known as c.7118T>G), located in coding exon 15 of the APC gene, results from a T to G substitution at nucleotide position 7118. The methionine at codon 2373 is replaced by arginine, an amino acid with similar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6501 samples (13002 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.003% (greater than 90000 alleles tested) in our clinical cohort. This amino acid position is not well conserved in available vertebrate species. 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 variant 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

ClinVar

Relating variation to medicine