NM_000038.6(APC):c.7026A>T (p.Leu2342Phe) AND Hereditary cancer-predisposing syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Feb 14, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000568988.13

Allele description

NM_000038.6(APC):c.7026A>T (p.Leu2342Phe)

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.7026A>T (p.Leu2342Phe)

HGVS:

NC_000005.10:g.112842620A>T
NG_008481.4:g.155100A>T
NM_000038.6:c.7026A>TMANE SELECT
NM_001127510.3:c.7026A>T
NM_001127511.3:c.6972A>T
NM_001354895.2:c.7026A>T
NM_001354896.2:c.7080A>T
NM_001354897.2:c.7056A>T
NM_001354898.2:c.6951A>T
NM_001354899.2:c.6942A>T
NM_001354900.2:c.6903A>T
NM_001354901.2:c.6849A>T
NM_001354902.2:c.6753A>T
NM_001354903.2:c.6723A>T
NM_001354904.2:c.6648A>T
NM_001354905.2:c.6546A>T
NM_001354906.2:c.6177A>T
NP_000029.2:p.Leu2342Phe
NP_001120982.1:p.Leu2342Phe
NP_001120983.2:p.Leu2324Phe
NP_001341824.1:p.Leu2342Phe
NP_001341825.1:p.Leu2360Phe
NP_001341826.1:p.Leu2352Phe
NP_001341827.1:p.Leu2317Phe
NP_001341828.1:p.Leu2314Phe
NP_001341829.1:p.Leu2301Phe
NP_001341830.1:p.Leu2283Phe
NP_001341831.1:p.Leu2251Phe
NP_001341832.1:p.Leu2241Phe
NP_001341833.1:p.Leu2216Phe
NP_001341834.1:p.Leu2182Phe
NP_001341835.1:p.Leu2059Phe
LRG_130:g.155100A>T
NC_000005.9:g.112178317A>T
NM_000038.5:c.7026A>T

Protein change:

L2059F

Links:

dbSNP: rs766086022

NCBI 1000 Genomes Browser:

rs766086022

Molecular consequence:

NM_000038.6:c.7026A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7026A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.6972A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7026A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7080A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7056A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.6951A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.6942A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.6903A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.6849A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.6753A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.6723A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.6648A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.6546A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6177A>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000667781	Ambry Genetics	criteria provided, single submitter (Ambry General Variant Classification Scheme_2022)	Uncertain significance (Feb 14, 2022)	germline	clinical testing	Citation Link,
SCV001346689	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (May 3, 2019)	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

SCV000667781

Ambry Genetics

criteria provided, single submitter

(Ambry General Variant Classification Scheme_2022)

Uncertain significance
(Feb 14, 2022)

germline

clinical testing

Citation Link,

SCV001346689

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(May 3, 2019)

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	1	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Ambry Genetics, SCV000667781.4

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

Description

The p.L2342F variant (also known as c.7026A>T), located in coding exon 15 of the APC gene, results from an A to T substitution at nucleotide position 7026. The leucine at codon 2342 is replaced by phenylalanine, an amino acid with highly similar properties. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. 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	1	not provided	not provided		1	not provided	not provided	not provided

From Color Diagnostics, LLC DBA Color Health, SCV001346689.1

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

#	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: Apr 20, 2024

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