NM_000038.6(APC):c.7676C>T (p.Pro2559Leu) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 18, 2019
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:: RCV002400466.2

Allele description [Variation Report for NM_000038.6(APC):c.7676C>T (p.Pro2559Leu)]

NM_000038.6(APC):c.7676C>T (p.Pro2559Leu)

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.7676C>T (p.Pro2559Leu)

HGVS:

NC_000005.10:g.112843270C>T
NG_008481.4:g.155750C>T
NM_000038.6:c.7676C>TMANE SELECT
NM_001127510.3:c.7676C>T
NM_001127511.3:c.7622C>T
NM_001354895.2:c.7676C>T
NM_001354896.2:c.7730C>T
NM_001354897.2:c.7706C>T
NM_001354898.2:c.7601C>T
NM_001354899.2:c.7592C>T
NM_001354900.2:c.7553C>T
NM_001354901.2:c.7499C>T
NM_001354902.2:c.7403C>T
NM_001354903.2:c.7373C>T
NM_001354904.2:c.7298C>T
NM_001354905.2:c.7196C>T
NM_001354906.2:c.6827C>T
NM_001407446.1:c.7760C>T
NM_001407447.1:c.7730C>T
NM_001407448.1:c.7730C>T
NM_001407449.1:c.7730C>T
NM_001407450.1:c.7676C>T
NM_001407451.1:c.7655C>T
NM_001407452.1:c.7646C>T
NM_001407453.1:c.7499C>T
NM_001407454.1:c.7427C>T
NM_001407455.1:c.7427C>T
NM_001407456.1:c.7427C>T
NM_001407457.1:c.7427C>T
NM_001407458.1:c.7373C>T
NM_001407459.1:c.7373C>T
NM_001407460.1:c.7373C>T
NM_001407467.1:c.7289C>T
NM_001407469.1:c.7289C>T
NM_001407470.1:c.6827C>T
NM_001407471.1:c.6524C>T
NM_001407472.1:c.6524C>T
NP_000029.2:p.Pro2559Leu
NP_000029.2:p.Pro2559Leu
NP_001120982.1:p.Pro2559Leu
NP_001120982.1:p.Pro2559Leu
NP_001120983.1:p.Pro2559Leu
NP_001120983.2:p.Pro2541Leu
NP_001341824.1:p.Pro2559Leu
NP_001341825.1:p.Pro2577Leu
NP_001341826.1:p.Pro2569Leu
NP_001341827.1:p.Pro2534Leu
NP_001341828.1:p.Pro2531Leu
NP_001341829.1:p.Pro2518Leu
NP_001341830.1:p.Pro2500Leu
NP_001341831.1:p.Pro2468Leu
NP_001341832.1:p.Pro2458Leu
NP_001341833.1:p.Pro2433Leu
NP_001341834.1:p.Pro2399Leu
NP_001341835.1:p.Pro2276Leu
NP_001394375.1:p.Pro2587Leu
NP_001394376.1:p.Pro2577Leu
NP_001394377.1:p.Pro2577Leu
NP_001394378.1:p.Pro2577Leu
NP_001394379.1:p.Pro2559Leu
NP_001394380.1:p.Pro2552Leu
NP_001394381.1:p.Pro2549Leu
NP_001394382.1:p.Pro2500Leu
NP_001394383.1:p.Pro2476Leu
NP_001394384.1:p.Pro2476Leu
NP_001394385.1:p.Pro2476Leu
NP_001394386.1:p.Pro2476Leu
NP_001394387.1:p.Pro2458Leu
NP_001394388.1:p.Pro2458Leu
NP_001394389.1:p.Pro2458Leu
NP_001394396.1:p.Pro2430Leu
NP_001394398.1:p.Pro2430Leu
NP_001394399.1:p.Pro2276Leu
NP_001394400.1:p.Pro2175Leu
NP_001394401.1:p.Pro2175Leu
LRG_130t1:c.7676C>T
LRG_130t2:c.7676C>T
LRG_130t3:c.7676C>T
LRG_130:g.155750C>T
LRG_130p1:p.Pro2559Leu
LRG_130p2:p.Pro2559Leu
LRG_130p3:p.Pro2559Leu
NC_000005.9:g.112178967C>T
NM_000038.4:c.7676C>T
NM_000038.5:c.7676C>T
NM_001127510.1:c.7676C>T
NM_001127511.1:c.7676C>T
NR_176365.1:n.7511C>T
NR_176366.1:n.7930C>T

Protein change:

P2175L

Molecular consequence:

NM_000038.6:c.7676C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.7676C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.7622C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.7676C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.7730C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.7706C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.7601C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.7592C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.7553C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.7499C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.7403C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.7373C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.7298C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.7196C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.6827C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407446.1:c.7760C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407447.1:c.7730C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407448.1:c.7730C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407449.1:c.7730C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407450.1:c.7676C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407451.1:c.7655C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407452.1:c.7646C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407453.1:c.7499C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407454.1:c.7427C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407455.1:c.7427C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407456.1:c.7427C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407457.1:c.7427C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407458.1:c.7373C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407459.1:c.7373C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407460.1:c.7373C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407467.1:c.7289C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407469.1:c.7289C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407470.1:c.6827C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407471.1:c.6524C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001407472.1:c.6524C>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

Clear Turn Off Turn On

HT 2
HT 2

biosample
poly(A) polymerase beta [Homo sapiens]
poly(A) polymerase beta [Homo sapiens]
gi|77874206|ref|NP_064529.4|

Protein

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
SCV002673140	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Sep 18, 2019)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002673140

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Sep 18, 2019)

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, SCV002673140.2

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

Description

The p.P2559L variant (also known as c.7676C>T), located in coding exon 15 of the APC gene, results from a C to T substitution at nucleotide position 7676. The proline at codon 2559 is replaced by leucine, an amino acid with similar properties. This amino acid position is highly 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 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

ClinVar

Relating variation to medicine