rs730881395
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_004655.4(AXIN2):c.1387C>T(p.Arg463Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000953 in 1,573,208 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R463G) has been classified as Uncertain significance.
Frequency
Consequence
NM_004655.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AXIN2 | NM_004655.4 | c.1387C>T | p.Arg463Cys | missense_variant | 6/11 | ENST00000307078.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AXIN2 | ENST00000307078.10 | c.1387C>T | p.Arg463Cys | missense_variant | 6/11 | 1 | NM_004655.4 | P1 | |
AXIN2 | ENST00000375702.5 | c.1387C>T | p.Arg463Cys | missense_variant | 5/9 | 1 | |||
AXIN2 | ENST00000618960.4 | c.1387C>T | p.Arg463Cys | missense_variant | 6/10 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 151962Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000108 AC: 2AN: 185328Hom.: 0 AF XY: 0.0000201 AC XY: 2AN XY: 99396
GnomAD4 exome AF: 0.00000985 AC: 14AN: 1421246Hom.: 0 Cov.: 37 AF XY: 0.0000114 AC XY: 8AN XY: 703704
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 151962Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74196
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2022 | The p.R463C variant (also known as c.1387C>T), located in coding exon 5 of the AXIN2 gene, results from a C to T substitution at nucleotide position 1387. The arginine at codon 463 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration has been reported in a family with attenuated familial adenomatous polyposis, without oligodontia or ectodermal dysplasia (Rivera B et al, Eur J Hum Genet. 2014 Mar;22:423-6). This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Uncertain significance, criteria provided, single submitter | curation | Sema4, Sema4 | Apr 30, 2021 | - - |
Oligodontia-cancer predisposition syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 07, 2023 | This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 463 of the AXIN2 protein (p.Arg463Cys). 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 familial adenomatous polyposis (AFAP). The variant segregates with disease in this family (PMID: 23838596). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 408788). 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 AXIN2 protein function with a negative predictive value of 80%. 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 | GeneDx | Dec 24, 2019 | In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Observed to segregate with disease in a family affected with attenuated familial adenomatous polyposis (AFAP) (Rivera 2014); This variant is associated with the following publications: (PMID: 25236910, 30671715, 29223984, 23838596) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at