NM_000038.6(APC):c.5366T>A (p.Val1789Glu) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 27, 2024
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:: RCV002348781.9

Allele description [Variation Report for NM_000038.6(APC):c.5366T>A (p.Val1789Glu)]

NM_000038.6(APC):c.5366T>A (p.Val1789Glu)

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.5366T>A (p.Val1789Glu)

HGVS:

NC_000005.10:g.112840960T>A
NG_008481.4:g.153440T>A
NM_000038.6:c.5366T>AMANE SELECT
NM_001127510.3:c.5366T>A
NM_001127511.3:c.5312T>A
NM_001354895.2:c.5366T>A
NM_001354896.2:c.5420T>A
NM_001354897.2:c.5396T>A
NM_001354898.2:c.5291T>A
NM_001354899.2:c.5282T>A
NM_001354900.2:c.5243T>A
NM_001354901.2:c.5189T>A
NM_001354902.2:c.5093T>A
NM_001354903.2:c.5063T>A
NM_001354904.2:c.4988T>A
NM_001354905.2:c.4886T>A
NM_001354906.2:c.4517T>A
NP_000029.2:p.Val1789Glu
NP_001120982.1:p.Val1789Glu
NP_001120983.2:p.Val1771Glu
NP_001341824.1:p.Val1789Glu
NP_001341825.1:p.Val1807Glu
NP_001341826.1:p.Val1799Glu
NP_001341827.1:p.Val1764Glu
NP_001341828.1:p.Val1761Glu
NP_001341829.1:p.Val1748Glu
NP_001341830.1:p.Val1730Glu
NP_001341831.1:p.Val1698Glu
NP_001341832.1:p.Val1688Glu
NP_001341833.1:p.Val1663Glu
NP_001341834.1:p.Val1629Glu
NP_001341835.1:p.Val1506Glu
LRG_130:g.153440T>A
NC_000005.9:g.112176657T>A
NM_000038.5:c.5366T>A

Protein change:

V1506E

Links:

dbSNP: rs1362525174

NCBI 1000 Genomes Browser:

rs1362525174

Molecular consequence:

NM_000038.6:c.5366T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127510.3:c.5366T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127511.3:c.5312T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354895.2:c.5366T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354896.2:c.5420T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354897.2:c.5396T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354898.2:c.5291T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354899.2:c.5282T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354900.2:c.5243T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354901.2:c.5189T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354902.2:c.5093T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354903.2:c.5063T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354904.2:c.4988T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354905.2:c.4886T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354906.2:c.4517T>A - 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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002646438	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Feb 27, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002646438

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Feb 27, 2024)

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, SCV002646438.2

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

Description

The p.V1789E variant (also known as c.5366T>A), located in coding exon 15 of the APC gene, results from a T to A substitution at nucleotide position 5366. The valine at codon 1789 is replaced by glutamic acid, an amino acid with dissimilar properties. This amino acid position is poorly conserved in available vertebrate species. In addition, in silico predictors for this gene do not accurately predict pathogenicity. Based on the available evidence, 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 12, 2024

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