rs876660265

chr5-112838678-T-Achr5-112838678-T-Cchr5-112838678-T-G

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM1 PM2 PM5 PP3 PP5_Very_Strong

The NM_000038.6(APC):c.3084T>A(p.Ser1028Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S1028I) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: APC NM_000038.6 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:3 U:2
• Conservation: PhyloP100: 0.962

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 15 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 16 uncertain 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 chr5-112838677-G-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 469904.Status of the report is reviewed_by_expert_panel, 3 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.829
• PP5: Variant 5-112838678-T-A is Pathogenic according to our data. Variant chr5-112838678-T-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 233215.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APC	NM_000038.6	c.3084T>A	p.Ser1028Arg	missense_variant	16/16	ENST00000257430.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APC	ENST00000257430.9	c.3084T>A	p.Ser1028Arg	missense_variant	16/16	5	NM_000038.6	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:3 Uncertain:2

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Mar 07, 2023	This missense variant replaces serine with arginine at codon 1028 of the APC protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant, however the residue is well conserved and may be important structurally (PMID: 18166348). This variant has not been reported in individuals affected with APC-related disorders in the literature, however the variant was reported as pathogenic in ClinVar based on multiple attenuated familial adenomatous polyposis cases (ClinVar Variation ID: VCV000233215; External laboratory communication). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	Jun 26, 2022	The p.S1028R pathogenic mutation (also known as c.3084T>A), located in coding exon 15 of the APC gene, results from a T to A substitution at nucleotide position 3084. The serine at codon 1028 is replaced by arginine, an amino acid with dissimilar properties. TThis alteration has been observed in multiple individuals with a personal and/or family history that is consistent with APC-related disease (Ambry internal data). In addition, another alteration at the same codon (p.S1028N) has been reported in at least one family with polyposis and was shown to segregate with disease (Ambry internal data). A nearby amino acid, APC p.N1026, likely interacts directly with APC p.S1028. A missense alteration at the nearby amino acid, APC p.N1026S, which was also shown to segregate with AFAP, is impaired in its ability to bind to β-Catenin and, thus, has reducing β-Catenin signaling (Menéndez M et al. Gastroenterology. 2008 Jan;134:56-64; Kohler EM et al. Hum. Mol. Genet. 2008 Jul;17:1978-87). This amino acid position is highly conserved in available vertebrate species. In addition, in silico predictors for this gene do not accurately predict pathogenicity. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Familial adenomatous polyposis 1 Pathogenic:1 Uncertain:1

Likely pathogenic, reviewed by expert panel	curation	ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel	Feb 25, 2023	The c.3084T>A variant in APC is a missense variant predicted to cause the substitution of serine by arginine at amino acid position 1028 p.(Ser1028Arg). This variant has been reported in 6 probands meeting phenotypic criteria, resulting in a total phenotype score of 3 (PS4_Moderate; Ambry Genetics internal data). This variant has been reported to segregate with FAP in 3 meioses in 2 families (6 meiosis in total) (PP1_Moderate; Ambry Genetics internal data). This variant is demonstrated to increased beta-catenin regulated transcription activity and decreased binding to bete-catenin by surface plasmon resonance (PS3_Supporting, Barcelona internal data). Another missense variant c.3083G>T (p.Ser1028Ile) in the same codon has been classified as Likely Pathogenic for FAP by the ClinGen InSiGHT Hereditary Colorectal Cancers/ Polyposis VCEP (PM5_Supporting). Finally, this variant is absent from gnomAD v2.1.1 (PM2_Supporting). In summary, this variant is classified as Likely Pathogenic for FAP based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel: PS4_Moderate, PP1_Moderate, PS3_Supporting, PM2_Supporting, PM5_Supporting (VCEP Specification version 1; date of approval: 12/12/2022). -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Oct 11, 2023	This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 1028 of the APC protein (p.Ser1028Arg). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with APC-related conditions. ClinVar contains an entry for this variant (Variation ID: 233215). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt APC protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Quest Diagnostics Nichols Institute San Juan Capistrano

Mar 08, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.48	D
BayesDel_noAF	Pathogenic	0.46
Cadd	Benign	23
Dann	Uncertain	1.0
Eigen	Benign	0.053
Eigen_PC	Benign	0.032
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Pathogenic	0.98	D;.;D;D
M_CAP	Pathogenic	0.35	D
MetaRNN	Pathogenic	0.83	D;D;D;D
MetaSVM	Pathogenic	0.94	D
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Pathogenic	0.90	D
PROVEAN	Uncertain	-2.8	D;N;N;N
REVEL	Pathogenic	0.74
Sift	Pathogenic	0.0	D;D;D;D
Sift4G	Uncertain	0.0050	D;D;D;D
Polyphen		1.0	.;D;D;.
Vest4		0.96, 0.81
MutPred		0.69		.;Gain of sheet (P = 0.0344);Gain of sheet (P = 0.0344);Gain of sheet (P = 0.0344);
MVP		1.0
ClinPred		0.91	D
GERP RS		-1.0
Varity_R		0.90
gMVP		0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs876660265; hg19: chr5-112174375; COSMIC: COSV57390656; COSMIC: COSV57390656;