17-65558144-A-T

Position:

• chr17-65558144-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_004655.4(AXIN2):​c.477T>A​(p.Asp159Glu) 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 benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: AXIN2 NM_004655.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.914

Genes affected

AXIN2 (HGNC:904): (axin 2) The Axin-related protein, Axin2, presumably plays an important role in the regulation of the stability of beta-catenin in the Wnt signaling pathway, like its rodent homologs, mouse conductin/rat axil. In mouse, conductin organizes a multiprotein complex of APC (adenomatous polyposis of the colon), beta-catenin, glycogen synthase kinase 3-beta, and conductin, which leads to the degradation of beta-catenin. Apparently, the deregulation of beta-catenin is an important event in the genesis of a number of malignancies. The AXIN2 gene has been mapped to 17q23-q24, a region that shows frequent loss of heterozygosity in breast cancer, neuroblastoma, and other tumors. Mutations in this gene have been associated with colorectal cancer with defective mismatch repair. [provided by RefSeq, Jul 2008]

ENSG00000266076 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.24334583).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AXIN2	NM_004655.4	c.477T>A	p.Asp159Glu	missense_variant	2/11	ENST00000307078.10	NP_004646.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AXIN2	ENST00000307078.10	c.477T>A	p.Asp159Glu	missense_variant	2/11	1	NM_004655.4	ENSP00000302625.5
ENSG00000266076	ENST00000577662.1	n.*653T>A		non_coding_transcript_exon_variant	4/7	2		ENSP00000462418.1
ENSG00000266076	ENST00000577662.1	n.*653T>A		3_prime_UTR_variant	4/7	2		ENSP00000462418.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.31
BayesDel_addAF	Benign	-0.13	T
BayesDel_noAF	Benign	-0.43
CADD	Benign	17
DANN	Benign	0.83
DEOGEN2	Benign	0.29	.;T;T;T;.;.
Eigen	Benign	-0.28
Eigen_PC	Benign	-0.31
FATHMM_MKL	Benign	0.71	D
LIST_S2	Benign	0.71	.;T;.;T;T;T
M_CAP	Benign	0.025	D
MetaRNN	Benign	0.24	T;T;T;T;T;T
MetaSVM	Benign	-1.2	T
PrimateAI	Uncertain	0.71	T
PROVEAN	Uncertain	-2.6	D;.;N;.;.;.
REVEL	Benign	0.20
Sift	Benign	0.17	T;.;T;.;.;.
Sift4G	Benign	0.14	T;T;T;.;.;.
Polyphen		1.0	.;D;D;.;.;.
Vest4		0.63
MutPred		0.31		Loss of ubiquitination at K162 (P = 0.1166);Loss of ubiquitination at K162 (P = 0.1166);Loss of ubiquitination at K162 (P = 0.1166);Loss of ubiquitination at K162 (P = 0.1166);Loss of ubiquitination at K162 (P = 0.1166);Loss of ubiquitination at K162 (P = 0.1166);
MVP		0.17
MPC		0.65
ClinPred		0.98	D
GERP RS		-0.24
gMVP		0.48

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-63554262;