NM_000038.6:c.1548G>C

Variant names:

• chr5-112827247-G-C
• rs879254090
• NM_000038.6:c.1548G>C

Variant summary

Our verdict is Pathogenic. The variant received 16 ACMG points: 16P and 0B. PM1 PM2 PP3_Strong PP5_Very_Strong

The NM_000038.6(APC):​c.1548G>C​(p.Lys516Asn) 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 (★★). Synonymous variant affecting the same amino acid position (i.e. K516K) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 33)
• Consequence: APC NM_000038.6 missense, splice_region
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:7
• Conservation: PhyloP100: 9.95
• Publications: 16 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

ENSG00000258864 (HGNC:):

ACMG classification

Our verdict: Pathogenic. The variant received 16 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 39 uncertain in NM_000038.6
• 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 5-112827247-G-C is Pathogenic according to our data. Variant chr5-112827247-G-C is described in ClinVar as Pathogenic. ClinVar VariationId is 246087.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.1548G>C	p.Lys516Asn	missense_variant, splice_region_variant	Exon 12 of 16	ENST00000257430.9	NP_000029.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APC	ENST00000257430.9	c.1548G>C	p.Lys516Asn	missense_variant, splice_region_variant	Exon 12 of 16	5	NM_000038.6	ENSP00000257430.4
ENSG00000258864	ENST00000520401.1	n.33G>C		splice_region_variant, non_coding_transcript_exon_variant	Exon 1 of 8	3		ENSP00000454861.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Familial adenomatous polyposis 1 Pathogenic:2

Jun 15, 2023

Myriad Genetics, Inc.

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered pathogenic. mRNA analysis has demonstrated abnormal mRNA splicing occurs [PMID: 17726045, Myriad internal data]. This variant has been reported in multiple individuals with clinical features of gene-specific disease [19196998, 20685668]. -

Aug 17, 2023

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This missense change has been observed in individuals with familial adenomatous polyposis (PMID: 8990002, 15300853, 15459959, 17489848, 20685668, 27000756). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 246087). 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 missense change results in skipping of exon 12 (also known as exon 11) and introduces a premature termination codon (PMID: 20685668, 24599579; Invitae). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces lysine, which is basic and polar, with asparagine, which is neutral and polar, at codon 516 of the APC protein (p.Lys516Asn). RNA analysis indicates that this missense change induces altered splicing and may result in an absent or disrupted protein product. -

not provided Pathogenic:2

Feb 18, 2022

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant at the last nucleotide of the exon demonstrated to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease (Lagarde 2010, Grandval 2014); Not observed at significant frequency in large population cohorts (gnomAD); Identified in patients with a personal and/or family history consistent with pathogenic variants in this gene referred for genetic testing at GeneDx and in published literature (van der Luijt 1997, Aretz 2004, Nielsen 2007, Crobach 2012, Liu 2016); This variant is associated with the following publications: (PMID: 15459959, 15300853, 21859464, 20564245, 20223039, 8990002, 27000756, 22000517, 20685668, 17489848, 20513532, 29901124, 22941256, 30414835, 18199528, 24599579) -

Jan 14, 2016

Clinical Genetics and Genomics, Karolinska University Hospital

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hereditary cancer-predisposing syndrome Pathogenic:2

May 23, 2024

Color Diagnostics, LLC DBA Color Health

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant changes the last nucleotide c.G of exon 12 of the APC gene and is predicted to impair RNA splicing at the intron 12 donor site. RT-PCR and minigene RNA analysis have shown that this variant causes out-of-frame skipping of exon 12 (coding exon 11) (PMID: 20685668, 24599579). This variant is expected to result in an absent or non-functional protein product. This variant has been reported in at least nine familial adenomatous polyposis kindreds (PMID: 8990002, 15300853, 15459959, 17489848, 20685668, 20564245, 22941256, 27000756). This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). Loss of APC function is a known mechanism of disease (clinicalgenome.org). Based on the available evidence, this variant is classified as Pathogenic. -

May 24, 2023

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1548G>C pathogenic mutation (also known as p.K516N), located in coding exon 11 of the APC gene, results from a G to C substitution at nucleotide position 1548. The amino acid change results in lysine to asparagine at codon 516, an amino acid with similar properties. However, this change occurs in the last base pair of coding exon 11, which makes it likely to have some effect on normal mRNA splicing. This mutation was originally reported in 2 unrelated Dutch FAP families (van der Luijt et al. Hum Mutat. 1997;9(1):7-16), and has since been reported in multiple FAP kindreds to date (Aretz S et al. Hum Mutat. 2004 Nov;24(5):370-80; Nielsen M et al. Clin Genet. 2007 May;71(5):427-33; Crobach S et al. Fam. Cancer 2012 Dec;11(4):671-3; Liu Q et al. Tumour Biol. 2016 Mar). In silico splice site analysis predicts that this alteration will result in the creation or strengthening of a novel splice donor site. However, one study found that a different alteration at the same location, c.1548G>A, caused complete skipping of exon 11 at the mRNA level (Kaufmann A et al. J Mol Diagn. 2009 Mar;11(2):131-9). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

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 p.Lys516Asn variant was identified in 7 of 3860 proband chromosomes (frequency: 0.002) from individuals or families with FAP or Attenuated-FAP, and was not identified in control chromosomes from healthy individuals (Nielsen 2007, Cowie 2004, Miclea 2010, Aretz 2004 15, van der Luijt 1997). The variant was also identified by our laboratory in 3 individuals with disease status not confirmed. The p.Lys516Asn variant was identified in the UMD Colon Genes database 11x and classified as causal and in the InSIGHT Colon cancer database, the variant was identified 6x and was classified 4x as pathogenic and 2x as unknown. The variant was not identified in the dbSNP nor in NHLBI Exome Sequencing Project (Exome Variant Server), Exome Aggregation Consortium (ExAC) database, COSMIC, MutDB, “Zhejiang Colon Cancer Database”, the ClinVar database, Clinvitae and GeneInsight COGR databases. The p.Lys516 residue is conserved across mammals and lower organisms, and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the Asparagine (Asn) variant may impact the protein. However, this information is not predictive enough to assume pathogenicity. The c.1548G>C 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 can affect splicing. In addition, 4 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer and HumanSpliceFinder) predict a greater than 10% difference in splicing. In one family, 17 patients were reported, there were more than 2 affected generations and 9 individuals had confirmed colon cancer, 2 had greater than 100 polyps and 10 had 10-100 polyps (Nielsen 2007). In addition, another variant at the same position c.1548G>A, was reported in one individual with FAP and transcript analysis demonstrated that the variant leads to complete skipping of exon 11 of the APC gene (c.1548G>A; r.1409_1548del; p.Gly471Tyrfs*19), increasing the likelihood that the c.1548G>C variant may result in aberrant splicing (Kaufmann 2009). In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.18	D
BayesDel_noAF	Uncertain	0.020
CADD	Pathogenic	36
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.94	.;D;D;D;D
Eigen	Pathogenic	0.92
Eigen_PC	Pathogenic	0.91
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Pathogenic	0.97	D;.;D;D;D
M_CAP	Benign	0.051	D
MetaRNN	Pathogenic	0.94	D;D;D;D;D
MetaSVM	Uncertain	-0.12	T
MutationAssessor	Benign	1.8	.;L;L;.;.
PhyloP100		9.9
PrimateAI	Pathogenic	0.86	D
PROVEAN	Pathogenic	-4.8	D;D;D;D;.
REVEL	Uncertain	0.63
Sift	Uncertain	0.0010	D;D;D;D;.
Sift4G	Uncertain	0.0020	D;D;D;D;D
Polyphen		1.0	.;D;D;.;.
Vest4		0.93, 0.89
MutPred		0.89		.;Loss of ubiquitination at K516 (P = 0.0161);Loss of ubiquitination at K516 (P = 0.0161);Loss of ubiquitination at K516 (P = 0.0161);.;
MVP		0.82
ClinPred		0.99	D
GERP RS		5.8
Varity_R		0.96
gMVP		0.84
Mutation Taster		=1/99	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.97
SpliceAI score (max)		0.65		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.64		Position offset: 38
DS_DL_spliceai		0.65		Position offset: 0

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

Other links and lift over

dbSNP: rs879254090; hg19: chr5-112162944;