NM_000038.6(APC):c.350C>A (p.Ser117Ter) AND Hereditary cancer-predisposing syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 16, 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:: RCV000561431.11

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)

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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Homo sapiens protein phosphatase 6 regulatory subunit 3 (PPP6R3), transcript var...
Homo sapiens protein phosphatase 6 regulatory subunit 3 (PPP6R3), transcript variant 41, non-coding RNA
gi|1677539176|ref|NR_147965.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000675927	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Pathogenic (Apr 16, 2021)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 11960572, 23159591, 25525159, 29122597 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000675927

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Pathogenic
(Apr 16, 2021)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

Citations

PubMed

Detection of sequence variations in the adenomatous polyposis coli (APC) gene using denaturing high-performance liquid chromatography.

Wu G, Wu W, Hegde M, Fawkner M, Chong B, Love D, Su LK, Lynch P, Snow K, Richards CS.

Genet Test. 2001 Winter;5(4):281-90.

PubMed [citation]

PMID:: 11960572

APC germline mutations in individuals being evaluated for familial adenomatous polyposis: a review of the Mayo Clinic experience with 1591 consecutive tests.

Kerr SE, Thomas CB, Thibodeau SN, Ferber MJ, Halling KC.

J Mol Diagn. 2013 Jan;15(1):31-43. doi: 10.1016/j.jmoldx.2012.07.005. Epub 2012 Nov 14. Review.

PubMed [citation]

PMID:: 23159591

See all PubMed Citations (4)

Details of each submission

From Ambry Genetics, SCV000675927.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

The p.S117* pathogenic mutation (also known as c.350C>A), located in coding exon 3 of the APC gene, results from a C to A substitution at nucleotide position 350. This changes the amino acid from a serine to a stop codon within coding exon 3. This mutation has been detected in multiple individuals with familial adenomatous polyposis (FAP) (Wu G et al. Genet. Test., 2001;5:281-90; Kerr SE et al. J Mol Diagn, 2013 Jan;15:31-43; Gutierrez Sanchez LH et al. Gastrointest Endosc, 2018 Mar;87:648-656.e3). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation.

#	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: Oct 8, 2024

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