5-112766410-G-T

Variant names:

• chr5-112766410-G-T
• rs876658941
• NM_000038.6:c.220G>T

Variant summary

Our verdict is Pathogenic. The variant received 22 ACMG points: 22P and 0B. PVS1 PM2 PP3_Strong PP5_Very_Strong

The NM_000038.6(APC):​c.220G>T​(p.Glu74*) variant causes a stop gained, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. E74E) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: APC NM_000038.6 stop_gained, splice_region
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:5
• Conservation: PhyloP100: 8.68
• Publications: 11 publications found

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]

APC Gene-Disease associations (from GenCC):

• classic or attenuated familial adenomatous polyposis

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• desmoid tumor

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Genomics England PanelApp
• familial adenomatous polyposis 1

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Ambry Genetics
• gastric adenocarcinoma and proximal polyposis of the stomach

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen, Orphanet
• sarcoma

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• APC-related attenuated familial adenomatous polyposis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Turcot syndrome with polyposis

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• Cenani-Lenz syndactyly syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Pathogenic. The variant received 22 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
• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 5-112766410-G-T is Pathogenic according to our data. Variant chr5-112766410-G-T is described in ClinVar as Pathogenic/Likely_pathogenic. ClinVar VariationId is 231074.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APC	NM_000038.6	c.220G>T	p.Glu74*	stop_gained, splice_region_variant	Exon 3 of 16	ENST00000257430.9	NP_000029.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APC	ENST00000257430.9	c.220G>T	p.Glu74*	stop_gained, splice_region_variant	Exon 3 of 16	5	NM_000038.6	ENSP00000257430.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 27

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial adenomatous polyposis 1 Pathogenic:2

Apr 08, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change creates a premature translational stop signal (p.Glu74*) in the APC gene. RNA analysis indicates that this premature translational stop signal induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with attenuated adenomatous polyposis (PMID: 17411426). ClinVar contains an entry for this variant (Variation ID: 231074). Studies have shown that this premature translational stop signal results in skipping of exon 3 and introduces a premature termination codon (Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -

Apr 25, 2023

Myriad Genetics, Inc.

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered pathogenic. This variant creates a termination codon and is predicted to result in premature protein truncation. -

Carcinoma of colon Pathogenic:1

-

Department of Pathology and Laboratory Medicine, Sinai Health System

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The APC p.Glu74X variant was identified in a family with an attenuated form of familial adenomatous polyposis (Schwarzova 2012). The p.Glu74X variant was also identified in HGMD, “InSiGHT Colon Cancer Database” and LOVD. This alteration would typically be predicted to result in a truncated or absent protein and loss of function; however, one study has demonstrated that for APC mutations closer to the 5’ terminus, an internal ribosome entry site is utilized to initiate translation at codon 184, resulting in a partially functional N-terminally truncated protein, which results in an attenuated phenotype (Heppner Goss 2002). The p.Glu74X variant occurs in the last base of the exon. This position has been shown to be part of the splicing consensus sequence and variants involving this position sometimes affect splicing. In a functional study by Schwarzova (2012), mRNA analysis showed that this variant created an aberrant splicing product which skipped exon 2 and could lead to expression of a truncated protein 48 amino acids long, or that would partly be subject to nonsense mediated decay. However, the authors of this study found another alternatively spliced APC transcript in all mRNA samples from control colon mucosa; this transcript was also found in the proband’s mRNA isolated from blood, but not in control blood samples. The authors suggest that the presence of this transcript in the patient’s blood may lead to the attenuated phenotype shown in the positive proband’s family. In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -

not provided Pathogenic:1

Nov 08, 2016

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is denoted APC c.220G>T at the cDNA level. Located in the last nucleotide of exon 3, it destroys a natural splice donor site and causes abnormal splicing. RNA analyses by Schwarzova et al. (2013) demonstrated that this variant results in skipping of exon 3, referred to as exon 2 using alternate nomenclature, as well as a second alternate transcript with skipping of exons 3 and 4 (also known as exons 2 and 3). These alternate transcripts may result in the production of some functional protein by using an alternate downstream AUG start codon at position 184. APC proteins produced from this alternate start codon have been shown to have normal cellular localization and ability to regulate B-catenin levels, which may explain the attenuated phenotype seen in some patients with 5' truncating APC variants (Heppner Goss 2002). APC c.220G>T has been seen in at least one individual with colorectal cancer who was reported to have attenuated familial adenomatous polyposis (AFAP), though the number of polyps was not described (Stekrova 2007). Although the nucleotide substitution is predicted to result in the change of a Glutamic Acid to a premature stop codon, and is called Glu74Ter in the literature, we are only using the nucleotide nomenclature to refer to the variant since it is not clear if any truncated protein from the premature stop codon is translated or if the observed abnormal splicing mitigates the effect of the premature stop codon. APC c.220G>T was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, suggesting it is not a common benign variant in these populations. Based on currently available evidence, we consider APC c.220G>T to be a likely pathogenic variant. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Nov 22, 2024

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.220G>T pathogenic mutation (also known as p.E74*), located in coding exon 2 of the APC gene, results from a G to T substitution at nucleotide position 220. This changes the amino acid from a glutamic acid to a stop codon within coding exon 2. This mutation has been reported in one or more individuals with attenuated FAP (Ambry internal data; Stekrova Jet al. BMC Med Genet. 2007 Apr 5;8:16). This change occurs in the last base pair of coding exon 2, which makes it likely to have some effect on normal mRNA splicing and RNA studies have shown that this alteration results in a transcript with out-of-frame skipping of coding exon 2 (Ambry internal data; Schwarzová L et al. Fam. Cancer 2013 Mar; 12(1):35-42). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site and will result in the creation or strengthening of a novel splice donor site. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. However, alterations that result in premature termination in coding exon 2 are associated with an attenuated phenotype and may have reduced penetrance compared to classic familial adenomatous polyposis syndrome. Clinical correlation is advised. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.66
CADD	Pathogenic	60
DANN	Uncertain	1.0
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.98
FATHMM_MKL	Pathogenic	1.0	D
M_CAP	Uncertain	0.097	D
PhyloP100		8.7
Vest4		0.88, 0.86
GERP RS		5.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		2.8
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	1.0
Splicevardb		3.0
SpliceAI score (max)		0.84		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.55		Position offset: 15
DS_DL_spliceai		0.84		Position offset: 0

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

Other links and lift over

dbSNP: rs876658941; hg19: chr5-112102107; COSMIC: COSV57345951;