NM_000038.6(APC):c.6383del (p.Ala2128fs) AND not provided

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 26, 2017
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:: RCV000115110.2

Allele description

NM_000038.6(APC):c.6383del (p.Ala2128fs)

Gene:

APC:APC regulator of WNT signaling pathway [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

5q22.2

Genomic location:

Preferred name:

NM_000038.6(APC):c.6383del (p.Ala2128fs)

HGVS:

NC_000005.10:g.112841977del
NG_008481.4:g.154457del
NM_000038.6:c.6383delMANE SELECT
NM_001127510.3:c.6383del
NM_001127511.3:c.6329del
NM_001354895.2:c.6383del
NM_001354896.2:c.6437del
NM_001354897.2:c.6413del
NM_001354898.2:c.6308del
NM_001354899.2:c.6299del
NM_001354900.2:c.6260del
NM_001354901.2:c.6206del
NM_001354902.2:c.6110del
NM_001354903.2:c.6080del
NM_001354904.2:c.6005del
NM_001354905.2:c.5903del
NM_001354906.2:c.5534del
NP_000029.2:p.Ala2128fs
NP_001120982.1:p.Ala2128fs
NP_001120983.2:p.Ala2110fs
NP_001341824.1:p.Ala2128fs
NP_001341825.1:p.Ala2146fs
NP_001341826.1:p.Ala2138fs
NP_001341827.1:p.Ala2103fs
NP_001341828.1:p.Ala2100fs
NP_001341829.1:p.Ala2087fs
NP_001341830.1:p.Ala2069fs
NP_001341831.1:p.Ala2037fs
NP_001341832.1:p.Ala2027fs
NP_001341833.1:p.Ala2002fs
NP_001341834.1:p.Ala1968fs
NP_001341835.1:p.Ala1845fs
LRG_130:g.154457del
NC_000005.9:g.112177674del
NM_000038.5:c.6383delC
p.A2128Vfs11

Protein change:

A1845fs

Links:

dbSNP: rs587779803

NCBI 1000 Genomes Browser:

rs587779803

Molecular consequence:

NM_000038.6:c.6383del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001127510.3:c.6383del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001127511.3:c.6329del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354895.2:c.6383del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354896.2:c.6437del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354897.2:c.6413del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354898.2:c.6308del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354899.2:c.6299del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354900.2:c.6260del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354901.2:c.6206del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354902.2:c.6110del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354903.2:c.6080del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354904.2:c.6005del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354905.2:c.5903del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001354906.2:c.5534del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000149019	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Dec 26, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000149019

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Dec 26, 2017)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000149019.5

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

Description

This deletion of one nucleotide in APC is denoted c.6383delC at the cDNA level and p.Ala2128ValfsX11 (A2128VfsX11) at the protein level. The normal sequence, with the base that is deleted in brackets, is CAAG[delC]TTCG. The deletion causes a frameshift which changes an Alanine to a Valine at codon 2128, and creates a premature stop codon at position 11 of the new reading frame. This variant is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. APC c.6383delC was identified in at least one individual with colon cancer (Susswein 2016). We consider this variant to be pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 14, 2021

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