NM_000038.6(APC):c.7457C>T (p.Pro2486Leu) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 20, 2021
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:: RCV003584487.1

Allele description [Variation Report for NM_000038.6(APC):c.7457C>T (p.Pro2486Leu)]

NM_000038.6(APC):c.7457C>T (p.Pro2486Leu)

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.7457C>T (p.Pro2486Leu)

HGVS:

NC_000005.10:g.112843051C>T
NG_008481.4:g.155531C>T
NM_000038.6:c.7457C>TMANE SELECT
NM_001127510.3:c.7457C>T
NM_001127511.3:c.7403C>T
NM_001354895.2:c.7457C>T
NM_001354896.2:c.7511C>T
NM_001354897.2:c.7487C>T
NM_001354898.2:c.7382C>T
NM_001354899.2:c.7373C>T
NM_001354900.2:c.7334C>T
NM_001354901.2:c.7280C>T
NM_001354902.2:c.7184C>T
NM_001354903.2:c.7154C>T
NM_001354904.2:c.7079C>T
NM_001354905.2:c.6977C>T
NM_001354906.2:c.6608C>T
NM_001407446.1:c.7541C>T
NM_001407447.1:c.7511C>T
NM_001407448.1:c.7511C>T
NM_001407449.1:c.7511C>T
NM_001407450.1:c.7457C>T
NM_001407451.1:c.7436C>T
NM_001407452.1:c.7427C>T
NM_001407453.1:c.7280C>T
NM_001407454.1:c.7208C>T
NM_001407455.1:c.7208C>T
NM_001407456.1:c.7208C>T
NM_001407457.1:c.7208C>T
NM_001407458.1:c.7154C>T
NM_001407459.1:c.7154C>T
NM_001407460.1:c.7154C>T
NM_001407467.1:c.7070C>T
NM_001407469.1:c.7070C>T
NM_001407470.1:c.6608C>T
NM_001407471.1:c.6305C>T
NM_001407472.1:c.6305C>T
NP_000029.2:p.Pro2486Leu
NP_000029.2:p.Pro2486Leu
NP_001120982.1:p.Pro2486Leu
NP_001120982.1:p.Pro2486Leu
NP_001120983.1:p.Pro2486Leu
NP_001120983.2:p.Pro2468Leu
NP_001341824.1:p.Pro2486Leu
NP_001341825.1:p.Pro2504Leu
NP_001341826.1:p.Pro2496Leu
NP_001341827.1:p.Pro2461Leu
NP_001341828.1:p.Pro2458Leu
NP_001341829.1:p.Pro2445Leu
NP_001341830.1:p.Pro2427Leu
NP_001341831.1:p.Pro2395Leu
NP_001341832.1:p.Pro2385Leu
NP_001341833.1:p.Pro2360Leu
NP_001341834.1:p.Pro2326Leu
NP_001341835.1:p.Pro2203Leu
NP_001394375.1:p.Pro2514Leu
NP_001394376.1:p.Pro2504Leu
NP_001394377.1:p.Pro2504Leu
NP_001394378.1:p.Pro2504Leu
NP_001394379.1:p.Pro2486Leu
NP_001394380.1:p.Pro2479Leu
NP_001394381.1:p.Pro2476Leu
NP_001394382.1:p.Pro2427Leu
NP_001394383.1:p.Pro2403Leu
NP_001394384.1:p.Pro2403Leu
NP_001394385.1:p.Pro2403Leu
NP_001394386.1:p.Pro2403Leu
NP_001394387.1:p.Pro2385Leu
NP_001394388.1:p.Pro2385Leu
NP_001394389.1:p.Pro2385Leu
NP_001394396.1:p.Pro2357Leu
NP_001394398.1:p.Pro2357Leu
NP_001394399.1:p.Pro2203Leu
NP_001394400.1:p.Pro2102Leu
NP_001394401.1:p.Pro2102Leu
LRG_130t1:c.7457C>T
LRG_130t2:c.7457C>T
LRG_130t3:c.7457C>T
LRG_130:g.155531C>T
LRG_130p1:p.Pro2486Leu
LRG_130p2:p.Pro2486Leu
LRG_130p3:p.Pro2486Leu
NC_000005.9:g.112178748C>T
NM_000038.4:c.7457C>T
NM_001127510.1:c.7457C>T
NM_001127511.1:c.7457C>T
NR_176365.1:n.7292C>T
NR_176366.1:n.7711C>T

Protein change:

P2102L

Molecular consequence:

NM_000038.6:c.7457C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7457C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7403C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7457C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7511C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7487C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7382C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7373C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.7334C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.7280C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.7184C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.7154C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.7079C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.6977C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6608C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407446.1:c.7541C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407447.1:c.7511C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407448.1:c.7511C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407449.1:c.7511C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407450.1:c.7457C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407451.1:c.7436C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407452.1:c.7427C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407453.1:c.7280C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407454.1:c.7208C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407455.1:c.7208C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407456.1:c.7208C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407457.1:c.7208C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407458.1:c.7154C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407459.1:c.7154C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407460.1:c.7154C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407467.1:c.7070C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407469.1:c.7070C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407470.1:c.6608C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407471.1:c.6305C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407472.1:c.6305C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_176365.1:n.7292C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176366.1:n.7711C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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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Caenibius tardaugens strain NBRC 16725 16S ribosomal RNA, partial sequence
Caenibius tardaugens strain NBRC 16725 16S ribosomal RNA, partial sequence
gi|631252671|gnl|REF_SSU16S|AB68111 410|ref|NR_113869.1|

Nucleotide
phosphoribosylformylglycinamidine synthase isoform X2 [Homo sapiens]
phosphoribosylformylglycinamidine synthase isoform X2 [Homo sapiens]
gi|2217312504|ref|XP_047292251.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004357557	Color Diagnostics, LLC DBA Color Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Dec 20, 2021)	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

SCV004357557

Color Diagnostics, LLC DBA Color Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Dec 20, 2021)

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

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 Color Diagnostics, LLC DBA Color Health, SCV004357557.1

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

Description

This missense variant replaces proline with leucine at codon 2486 of the APC protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is 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: Feb 20, 2024

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