rs1060503318

chr5-112835165-G-Achr5-112835165-G-Cchr5-112835165-G-T

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000038.6(APC):c.1958G>A(p.Arg653Lys) variant causes a missense, 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 Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R653G) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: APC NM_000038.6 missense, splice_region
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:4
• Conservation: PhyloP100: 9.60

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]

ACMG classification

Verdict is Pathogenic. Variant got 18 ACMG points.

• PM1: In a helix (size 8) in uniprot entity APC_HUMAN there are 11 pathogenic changes around while only 2 benign (85%) in NM_000038.6
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr5-112835164-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 428139.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 5-112835165-G-A is Pathogenic according to our data. Variant chr5-112835165-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 428128.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-112835165-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APC	NM_000038.6	c.1958G>A	p.Arg653Lys	missense_variant, splice_region_variant	15/16	ENST00000257430.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APC	ENST00000257430.9	c.1958G>A	p.Arg653Lys	missense_variant, splice_region_variant	15/16	5	NM_000038.6	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Carcinoma of colon Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

Department of Pathology and Laboratory Medicine, Sinai Health System

-

The APC p.Arg653Lys variant was identified in 7 of 15446 proband chromosomes (frequency: 0.0005) from individuals or families with familial colorectal adenomas and colorectal cancer and was not identified in 1938 control chromosomes from healthy individuals (Azzopardi 2008, Inra 2015, Lagarde 2010). The variant was also identified in ClinVar (classified as pathogenic by Invitae; as likely pathogenic by Ambry Genetics), Cosmic (4x in large intestine), LOVD 3.0 (1x as affects function), and in UMD-LSDB (8x causal) databases. The variant was not identified in dbSNP, COGR, MutDB, or Zhejiang University 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.Arg653 residue is conserved across mammals and other organisms, and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The p.Arg653Lys variant occurs in the last three bases 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 addition, 5 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing. In addition, in vitro analysis by RT-PCR and ex vivo analysis by Splicing reporter minigene pCAS, showed major loss of exon 14 during splicing (Grandval 2014). In summary, based on the above information this variant meets our laboratory’s criteria to be classified as pathogenic. -

Familial adenomatous polyposis 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Dec 05, 2023

This sequence change affects codon 653 of the APC mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the APC protein. RNA analysis indicates that this variant induces altered splicing and likely disrupts the C-terminus of the protein. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with familial adenomatous polyposis and colorectal cancer (PMID: 18199528, 20685668, 24599579, 25590978). ClinVar contains an entry for this variant (Variation ID: 428128). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 15 (also known as exon 14) and introduces a new termination codon (PMID: 20685668, 24599579). However the mRNA is not expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Quest Diagnostics Nichols Institute San Juan Capistrano

Oct 08, 2020

This variant has been reported in in individuals with colorectal adenomas in the published literature (PMIDs: 18199528 (2008) and 20685668 (2010)). This variant also causes exon 15 skipping (PMID: 20685668 (2010)). Additional analysis using software algorithms for the prediction of the effect of nucleotide changes on splicing yielded predictions that this variant may affect proper APC mRNA splicing . Therefore, the variant is classified as pathogenic. -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 03, 2022

The c.1958G>A pathogenic variant (also known as p.R653K) is located in coding exon 14 of the APC gene. This variant results from a G to A substitution at nucleotide position 1958. The amino acid change results in arginine to lysine at codon 653, an amino acid with highly similar properties. This change occurs in the last base pair of coding exon 14 which makes it likely to have some effect on normal mRNA splicing. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. This alteration, as well as a close match alteration, c.1958G>T, has been detected in multiple patients with FAP (Azzopardi D et al. Cancer Res. 2008 Jan 15;68(2):358-63; Minde DP et al. Mol Cancer. 2011 Aug 22;10:101; ). RNA studies have demonstrated that this alteration, as well as a close match alteration, c.1958G>T, results in abnormal splicing in the set of samples tested (Ambry internal data; Lagarde A et al. J. Med. Genet., 2010 Oct;47:721-2; Ambry internal data). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.95
BayesDel_addAF	Pathogenic	0.35	D
BayesDel_noAF	Pathogenic	0.27
Cadd	Pathogenic	34
Dann	Uncertain	1.0
Eigen	Pathogenic	0.90
Eigen_PC	Pathogenic	0.86
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Uncertain	0.93	D;.;D;D;D
M_CAP	Uncertain	0.17	D
MetaRNN	Pathogenic	0.89	D;D;D;D;D
MetaSVM	Uncertain	0.065	D
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Pathogenic	0.89	D
PROVEAN	Uncertain	-2.9	D;D;D;D;.
REVEL	Pathogenic	0.75
Sift	Uncertain	0.029	D;D;D;D;.
Sift4G	Uncertain	0.037	D;D;D;D;D
Polyphen		1.0	.;D;D;.;.
Vest4		0.88, 0.67
MutPred		0.80		.;Gain of ubiquitination at R653 (P = 0.0198);Gain of ubiquitination at R653 (P = 0.0198);Gain of ubiquitination at R653 (P = 0.0198);.;
MVP		0.93
ClinPred		0.99	D
GERP RS		5.2
Varity_R		0.95
gMVP		0.86

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	1.0
SpliceAI score (max)		0.98		Details are displayed if max score is > 0.2
DS_DL_spliceai		0.98		Position offset: 0

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

Publications

LitVar

Other links and lift over

dbSNP: rs1060503318; hg19: chr5-112170862; COSMIC: COSV57333087;