17-3664718-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_014604.4(TAX1BP3):c.120T>C(p.Asp40=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.87 in 1,613,640 control chromosomes in the GnomAD database, including 612,156 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.85 ( 55486 hom., cov: 32)

Exomes 𝑓: 0.87 ( 556670 hom. )

Consequence

TAX1BP3
NM_014604.4 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.329

Variant links:

Genes affected

TAX1BP3 (HGNC:30684): (Tax1 binding protein 3) This gene encodes a small, highly conserved protein with a single PDZ domain. PDZ (PSD-95/Discs large/ZO-1 homologous) domains promote protein-protein interactions that affect cell signaling, adhesion, protein scaffolding, and receptor and ion transporter functions. The encoded protein interacts with a large number of target proteins that play roles in signaling pathways; for example, it interacts with Rho A and glutaminase L and also acts as a negative regulator of the Wnt/beta-catenin signaling pathway. This protein was first identified as binding to the T-cell leukaemia virus (HTLV1) Tax oncoprotein. Overexpression of this gene has been implicated in altered cancer cell adhesion, migration and metastasis. The encoded protein also modulates the localization and density of inwardly rectifying potassium channel 2.3 (Kir2.3). To date, this protein has been shown to play a role in cell proliferation, development, stress response, and polarization. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Apr 2017]

TAX1BP3 links:

P2RX5-TAX1BP3 (HGNC:):

P2RX5-TAX1BP3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 17-3664718-A-G is Benign according to our data. Variant chr17-3664718-A-G is described in ClinVar as [Benign]. Clinvar id is 1577462.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.329 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.885 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
TAX1BP3	NM_014604.4 linkuse as main transcript	c.120T>C	p.Asp40=	synonymous_variant	2/4	ENST00000225525.4
P2RX5-TAX1BP3	NR_037928.1 linkuse as main transcript	n.5175T>C		non_coding_transcript_exon_variant	13/15
TAX1BP3	NM_001204698.2 linkuse as main transcript	c.120T>C	p.Asp40=	synonymous_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TAX1BP3	ENST00000225525.4 linkuse as main transcript	c.120T>C	p.Asp40=	synonymous_variant	2/4	1	NM_014604.4	P1
TAX1BP3	ENST00000611779.4 linkuse as main transcript	c.120T>C	p.Asp40=	synonymous_variant	2/3	2

Frequencies

GnomAD3 genomes

AF:

0.852

AC:

129570

AN:

151994

Hom.:

55468

Cov.:

show subpopulations

Gnomad AFR

AF:

0.812

Gnomad AMI

AF:

0.913

Gnomad AMR

AF:

0.842

Gnomad ASJ

AF:

0.908

Gnomad EAS

AF:

0.693

Gnomad SAS

AF:

0.778

Gnomad FIN

AF:

0.866

Gnomad MID

AF:

0.861

Gnomad NFE

AF:

0.891

Gnomad OTH

AF:

0.860

GnomAD3 exomes

AF:

0.844

AC:

212024

AN:

251212

Hom.:

89978

AF XY:

0.845

AC XY:

114775

AN XY:

135844

show subpopulations

Gnomad AFR exome

AF:

0.810

Gnomad AMR exome

AF:

0.795

Gnomad ASJ exome

AF:

0.906

Gnomad EAS exome

AF:

0.700

Gnomad SAS exome

AF:

0.782

Gnomad FIN exome

AF:

0.874

Gnomad NFE exome

AF:

0.892

Gnomad OTH exome

AF:

0.856

GnomAD4 exome

AF:

0.872

AC:

1273731

AN:

1461528

Hom.:

556670

Cov.:

AF XY:

0.869

AC XY:

632012

AN XY:

727050

show subpopulations

Gnomad4 AFR exome

AF:

0.813

Gnomad4 AMR exome

AF:

0.800

Gnomad4 ASJ exome

AF:

0.904

Gnomad4 EAS exome

AF:

0.710

Gnomad4 SAS exome

AF:

0.783

Gnomad4 FIN exome

AF:

0.871

Gnomad4 NFE exome

AF:

0.889

Gnomad4 OTH exome

AF:

0.854

GnomAD4 genome

AF:

0.852

AC:

129630

AN:

152112

Hom.:

55486

Cov.:

AF XY:

0.848

AC XY:

63084

AN XY:

74348

show subpopulations

Gnomad4 AFR

AF:

0.812

Gnomad4 AMR

AF:

0.842

Gnomad4 ASJ

AF:

0.908

Gnomad4 EAS

AF:

0.693

Gnomad4 SAS

AF:

0.778

Gnomad4 FIN

AF:

0.866

Gnomad4 NFE

AF:

0.891

Gnomad4 OTH

AF:

0.852

Alfa

AF:

0.880

Hom.:

29962

Bravo

AF:

0.849

Asia WGS

AF:

0.705

AC:

2455

AN:

3478

EpiCase

AF:

0.886

EpiControl

AF:

0.890

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

Cadd

Benign

Dann

Benign

0.83

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over