rs762872515
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_004655.4(AXIN2):c.2141G>A(p.Arg714Gln) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000056 in 1,607,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R714W) has been classified as Likely benign.
Frequency
Consequence
NM_004655.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AXIN2 | NM_004655.4 | c.2141G>A | p.Arg714Gln | missense_variant, splice_region_variant | 8/11 | ENST00000307078.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AXIN2 | ENST00000307078.10 | c.2141G>A | p.Arg714Gln | missense_variant, splice_region_variant | 8/11 | 1 | NM_004655.4 | P1 | |
AXIN2 | ENST00000375702.5 | c.1946G>A | p.Arg649Gln | missense_variant, splice_region_variant | 6/9 | 1 | |||
AXIN2 | ENST00000618960.4 | c.1946G>A | p.Arg649Gln | missense_variant, splice_region_variant | 7/10 | 5 | |||
AXIN2 | ENST00000578251.1 | n.363G>A | splice_region_variant, non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152248Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000861 AC: 2AN: 232212Hom.: 0 AF XY: 0.0000158 AC XY: 2AN XY: 126294
GnomAD4 exome AF: 0.00000481 AC: 7AN: 1455750Hom.: 0 Cov.: 32 AF XY: 0.00000553 AC XY: 4AN XY: 723700
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152248Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74388
ClinVar
Submissions by phenotype
Oligodontia-cancer predisposition syndrome Uncertain:2
Uncertain significance, no assertion criteria provided | clinical testing | Molecular Oncology Laboratory, Hospital Clínico San Carlos | Jun 01, 2018 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 09, 2024 | This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 714 of the AXIN2 protein (p.Arg714Gln). This variant also falls at the last nucleotide of exon 8, which is part of the consensus splice site for this exon. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with attenuated adenomatous polyposis (PMID: 31285513). ClinVar contains an entry for this variant (Variation ID: 422352). 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). RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (Invitae). 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. - |
Hereditary cancer-predisposing syndrome Uncertain:2
Uncertain significance, criteria provided, single submitter | curation | Sema4, Sema4 | Aug 17, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2024 | The c.2141G>A variant (also known as p.R714Q), located in coding exon 7 of the AXIN2 gene, results from a G to A substitution at nucleotide position 2141. The amino acid change results in arginine to glutamine at codon 714, an amino acid with highly similar properties. However, this change occurs in the last base pair of coding exon 7, which makes it likely to have some effect on normal mRNA splicing. In a cohort study comprised of 158 attenuated adenomatous polyposis patients, this variant was identified once in a proband diagnosed with colorectal cancer as well as over 10 adenomatous polyps at age 72 and this variant segregated with disease in one family member (Lorca V et al. Sci Rep, 2019 07;9:9814). This nucleotide position is highly conserved in available vertebrate species. In silico splice site analysis for this alteration is inconclusive. In addition, the missense variant is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Sep 27, 2016 | This variant is denoted AXIN2 c.2141G>A at the cDNA level, p.Arg714Gln (R714Q) at the protein level, and results in the change of an Arginine to a Glutamine (CGG>CAG). This variant has not, to our knowledge, been published in the literature as pathogenic or benign. AXIN2 Arg714Gln 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. Since Arginine and Glutamine differ in some properties, this is considered a semi-conservative amino acid substitution. AXIN2 Arg714Gln occurs at a position that is conserved in mammals and is located in the within mutational hot spot exon (Salahshor 2005). In silico analyses are inconsistent regarding the effect this variant may have on protein structure and function. Based on currently available evidence, it is unclear whether AXIN2 Arg714Gln is a pathogenic or benign variant. We consider it to be a variant of uncertain significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at