rs863224820

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong

The NM_000038.6(APC):​c.453delA​(p.Glu152fs) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 32)

Consequence

APC
NM_000038.6 frameshift

Scores

Not classified

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:6

Conservation

PhyloP100: 8.57
Variant links:
Genes affected
APC (HGNC:583): (APC regulator of WNT signaling pathway) This gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt signaling pathway. It is also involved in other processes including cell migration and adhesion, transcriptional activation, and apoptosis. Defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy. Mutations in the APC gene have been found to occur in most colorectal cancers, where disease-associated mutations tend to be clustered in a small region designated the mutation cluster region (MCR) and result in a truncated protein product. [provided by RefSeq, Jun 2022]

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 5-112775657-GA-G is Pathogenic according to our data. Variant chr5-112775657-GA-G is described in ClinVar as [Pathogenic]. Clinvar id is 216848.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112775657-GA-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
APCNM_000038.6 linkuse as main transcriptc.453delA p.Glu152fs frameshift_variant 5/16 ENST00000257430.9 NP_000029.2 P25054-1Q4LE70

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
APCENST00000257430.9 linkuse as main transcriptc.453delA p.Glu152fs frameshift_variant 5/165 NM_000038.6 ENSP00000257430.4 P25054-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Familial adenomatous polyposis 1 Pathogenic:2
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpOct 12, 2023This sequence change creates a premature translational stop signal (p.Glu152Lysfs*18) in the APC gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in APC are known to be pathogenic (PMID: 17963004, 20685668). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with familial adenomatous polyposis and hepatoblastoma (PMID: 12702169, 20223039, 23575299, 23715166). ClinVar contains an entry for this variant (Variation ID: 216848). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitterclinical testingMyriad Genetics, Inc.Apr 26, 2023This variant is considered pathogenic. This variant creates a frameshift predicted to result in premature protein truncation. -
not provided Pathogenic:2
Pathogenic, no assertion criteria providedresearchMayo Clinic Laboratories, Mayo Clinic-- -
Pathogenic, criteria provided, single submitterclinical testingGeneDxDec 06, 2021Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (Lek 2016); This variant is associated with the following publications: (PMID: 12702169, 28185118, 20223039, 29251405, 23575299, 32543227, 23715166) -
Carcinoma of colon Pathogenic:1
Pathogenic, no assertion criteria providedclinical testingDepartment of Pathology and Laboratory Medicine, Sinai Health System-The APC p.Glu152LysfsX18 variant was identified in 3 of 3892 proband chromosomes (frequency: 0.0008) from individuals or families with FAP (Friedl_2005, Heinitz_2003, Mankay_2017). The variant was also identified in the following databases: dbSNP (ID: rs863224820) as “With Pathogenic allele”, and in ClinVar (4x as pathogenic by Invitae, GeneDx, Ambry Genetics, Mayo Clinic, criteria provided). The variant was not identified in Cosmic, MutDB, LOVD 3.0, UMD-LSDB, Zhejiang Colon Cancer Database, databases. The variant was not identified in the following control databases: the 1000 Genomes Project, the NHLBI GO Exome Sequencing Project, the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The p.Glu152LysfsX18 variant was identified in a patient as co-occurring with a different germline missense variant E1317Q (Heinitz_2003). The p.Glu152LysfsX18 variant was observed in a young child (18 month) affected with hepatoblastoma (Gupta_2013), and a 12 year old girl from a FAP family who was diagnosed with extraintestinal malignancy (Rauch_2014). The c.453del variant is predicted to cause a frameshift, which alters the protein's amino acid sequence beginning at codon 152 and leads to a premature stop codon 18 codons downstream. This alteration is then predicted to result in a truncated or absent protein and loss of function. Loss of function variants of the APC gene are an established mechanism of disease in FAP and is the type of variant expected to cause the disorder. In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic. -
Hereditary cancer-predisposing syndrome Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingAmbry GeneticsApr 27, 2023The c.453delA pathogenic mutation, located in coding exon 4 of the APC gene, results from a deletion of one nucleotide at nucleotide position 453, causing a translational frameshift with a predicted alternate stop codon (p.E152Kfs*18). This mutation has been detected in multiple patients with a clinical diagnosis of familial adenomatous polyposis (FAP) (Heinritz W et al. Clin. Genet. 2003 Apr; 63(4):325-7; Friedl W and Aretz S. Hered Cancer Clin Pract. 2005 Sep; 3(3):95-114; Mankaney G et al. Fam. Cancer. 2017 Feb; Pegues J et al. Ear Nose Throat J, 2020 Jun;:145561320934602). It has also been detected in a child who presented with multifocal hepatic neoplasia at 18 months of age (Gupta A et al. Am. J. Surg. Pathol. 2013 Jul; 37(7):1058-66) and in another child who was diagnosed with FAP at age 10 and presented with Cushing syndrome due to an adrenocortical carcinoma at age 12 (Rauch LB et al. J. Pediatr. Gastroenterol. Nutr. 2014 Feb; 58(2):e19-20). 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. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.54
Details are displayed if max score is > 0.2
DS_AL_spliceai
0.54
Position offset: -28

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs863224820; hg19: chr5-112111354; API