NM_000038.6(APC):c.350C>A (p.Ser117Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 18, 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:: RCV000482015.10

Allele description [Variation Report for NM_000038.6(APC):c.350C>A (p.Ser117Ter)]

NM_000038.6(APC):c.350C>A (p.Ser117Ter)

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.350C>A (p.Ser117Ter)

HGVS:

NC_000005.10:g.112767318C>A
NG_008481.4:g.79798C>A
NM_000038.6:c.350C>AMANE SELECT
NM_001127510.3:c.350C>A
NM_001127511.3:c.380C>A
NM_001354895.2:c.350C>A
NM_001354896.2:c.350C>A
NM_001354897.2:c.380C>A
NM_001354898.2:c.275C>A
NM_001354899.2:c.350C>A
NM_001354900.2:c.173C>A
NM_001354901.2:c.173C>A
NM_001354902.2:c.380C>A
NM_001354903.2:c.350C>A
NM_001354904.2:c.275C>A
NM_001354905.2:c.173C>A
NM_001354906.2:c.-686C>A
NP_000029.2:p.Ser117Ter
NP_001120982.1:p.Ser117Ter
NP_001120983.2:p.Ser127Ter
NP_001341824.1:p.Ser117Ter
NP_001341825.1:p.Ser117Ter
NP_001341826.1:p.Ser127Ter
NP_001341827.1:p.Ser92Ter
NP_001341828.1:p.Ser117Ter
NP_001341829.1:p.Ser58Ter
NP_001341830.1:p.Ser58Ter
NP_001341831.1:p.Ser127Ter
NP_001341832.1:p.Ser117Ter
NP_001341833.1:p.Ser92Ter
NP_001341834.1:p.Ser58Ter
LRG_130:g.79798C>A
NC_000005.9:g.112103015C>A
NM_000038.5:c.350C>A

Protein change:

S117*

Links:

dbSNP: rs1064793535

NCBI 1000 Genomes Browser:

rs1064793535

Molecular consequence:

NM_001354906.2:c.-686C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000038.6:c.350C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001127510.3:c.350C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001127511.3:c.380C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354895.2:c.350C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354896.2:c.350C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354897.2:c.380C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354898.2:c.275C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354899.2:c.350C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354900.2:c.173C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354901.2:c.173C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354902.2:c.380C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354903.2:c.350C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354904.2:c.275C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354905.2:c.173C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000566355	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Pathogenic (Oct 18, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000566355

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Pathogenic
(Oct 18, 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, SCV000566355.5

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

Description

This pathogenic variant is denoted APC c.350C>A at the cDNA level and p.Ser117Ter (S117X) at the protein level. The substitution creates a nonsense variant, which changes a Serine to a premature stop codon (TCA>TAA), and is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. This variant has been reported in association with attenuated Familial Adenomatous Polyposis (Kerr 2013) and is considered 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: Nov 3, 2024

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