NM_000038.6(APC):c.959C>A (p.Ser320Ter) AND Familial multiple polyposis syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 29, 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:: RCV003988110.1

Allele description [Variation Report for NM_000038.6(APC):c.959C>A (p.Ser320Ter)]

NM_000038.6(APC):c.959C>A (p.Ser320Ter)

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.959C>A (p.Ser320Ter)

HGVS:

NC_000005.10:g.112818991C>A
NG_008481.4:g.131471C>A
NM_000038.6:c.959C>AMANE SELECT
NM_001127510.3:c.959C>A
NM_001127511.3:c.905C>A
NM_001354895.2:c.959C>A
NM_001354896.2:c.959C>A
NM_001354897.2:c.989C>A
NM_001354898.2:c.884C>A
NM_001354899.2:c.875C>A
NM_001354900.2:c.782C>A
NM_001354901.2:c.782C>A
NM_001354902.2:c.964-278C>A
NM_001354903.2:c.934-278C>A
NM_001354904.2:c.859-278C>A
NM_001354905.2:c.757-278C>A
NM_001354906.2:c.110C>A
NM_001407446.1:c.989C>A
NM_001407447.1:c.959C>A
NM_001407448.1:c.959C>A
NM_001407449.1:c.959C>A
NM_001407450.1:c.959C>A
NM_001407451.1:c.884C>A
NM_001407452.1:c.875C>A
NM_001407453.1:c.782C>A
NM_001407454.1:c.934-278C>A
NM_001407455.1:c.934-278C>A
NM_001407456.1:c.934-278C>A
NM_001407457.1:c.934-278C>A
NM_001407458.1:c.934-278C>A
NM_001407459.1:c.934-278C>A
NM_001407460.1:c.934-278C>A
NM_001407467.1:c.850-278C>A
NM_001407469.1:c.850-278C>A
NM_001407470.1:c.110C>A
NM_001407471.1:c.85-278C>A
NM_001407472.1:c.85-278C>A
NP_000029.2:p.Ser320Ter
NP_000029.2:p.Ser320Ter
NP_001120982.1:p.Ser320Ter
NP_001120982.1:p.Ser320Ter
NP_001120983.1:p.Ser320Ter
NP_001120983.2:p.Ser302Ter
NP_001341824.1:p.Ser320Ter
NP_001341825.1:p.Ser320Ter
NP_001341826.1:p.Ser330Ter
NP_001341827.1:p.Ser295Ter
NP_001341828.1:p.Ser292Ter
NP_001341829.1:p.Ser261Ter
NP_001341830.1:p.Ser261Ter
NP_001341835.1:p.Ser37Ter
NP_001394375.1:p.Ser330Ter
NP_001394376.1:p.Ser320Ter
NP_001394377.1:p.Ser320Ter
NP_001394378.1:p.Ser320Ter
NP_001394379.1:p.Ser320Ter
NP_001394380.1:p.Ser295Ter
NP_001394381.1:p.Ser292Ter
NP_001394382.1:p.Ser261Ter
NP_001394399.1:p.Ser37Ter
LRG_130t1:c.959C>A
LRG_130t2:c.959C>A
LRG_130t3:c.959C>A
LRG_130:g.131471C>A
LRG_130p1:p.Ser320Ter
LRG_130p2:p.Ser320Ter
LRG_130p3:p.Ser320Ter
NC_000005.9:g.112154688C>A
NM_000038.4:c.959C>A
NM_001127510.1:c.959C>A
NM_001127511.1:c.959C>A
NR_176365.1:n.1129C>A
NR_176366.1:n.1548C>A

Protein change:

S261*

Molecular consequence:

NM_001354902.2:c.964-278C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354903.2:c.934-278C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354904.2:c.859-278C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001354905.2:c.757-278C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407454.1:c.934-278C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407455.1:c.934-278C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407456.1:c.934-278C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407457.1:c.934-278C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407458.1:c.934-278C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407459.1:c.934-278C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407460.1:c.934-278C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407467.1:c.850-278C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407469.1:c.850-278C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407471.1:c.85-278C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001407472.1:c.85-278C>A - intron variant - [Sequence Ontology: SO:0001627]
NR_176365.1:n.1129C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_176366.1:n.1548C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000038.6:c.959C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001127510.3:c.959C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001127511.3:c.905C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354895.2:c.959C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354896.2:c.959C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354897.2:c.989C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354898.2:c.884C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354899.2:c.875C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354900.2:c.782C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354901.2:c.782C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001354906.2:c.110C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001407446.1:c.989C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001407447.1:c.959C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001407448.1:c.959C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001407449.1:c.959C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001407450.1:c.959C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001407451.1:c.884C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001407452.1:c.875C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001407453.1:c.782C>A - nonsense - [Sequence Ontology: SO:0001587]
NM_001407470.1:c.110C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Familial multiple polyposis syndrome (FAP)
Synonyms:: Familial adenomatous polyposis of the colon; Familial polyposis of the colon; Familial intestinal polyposis; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0021055; MedGen: C0032580; OMIM: PS175100

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lipopolysaccharide assembly protein LapB [Burkholderia vietnamiensis]
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004803831	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Pathogenic (Jan 29, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004803831

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Pathogenic
(Jan 29, 2024)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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

Molecular characterization of colorectal cancer using whole-exome sequencing in a Taiwanese population.

Chang YS, Lee CC, Ke TW, Chang CM, Chao DS, Huang HY, Chang JG.

Cancer Med. 2019 Jul;8(8):3738-3747. doi: 10.1002/cam4.2282. Epub 2019 May 24.

PubMed [citation]

PMID:: 31127692
PMCID:: PMC6639182

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004803831.1

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

Description

Variant summary: APC c.959C>A (p.Ser320X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The frequency data for this variant in gnomAD is considered unreliable, as metrics indicate poor data quality at this position. c.959C>A has been reported in the literature in at least one individual affected with colorectal cancer (e.g. Chang_2018). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication have been ascertained in the context of this evaluation (PMID: 31127692). ClinVar contains an entry for this variant (Variation ID: 2583947). Based on the evidence outlined above, the variant was classified as pathogenic.

#	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: Nov 3, 2024

ClinVar

Relating variation to medicine