Variant X-105220312-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_031274.5(TEX13A):c.86C>T(p.Thr29Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000164 in 1,096,701 control chromosomes in the GnomAD database, including 1 homozygotes. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/15 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: 23)

Exomes 𝑓: 0.000016 ( 1 hom. 6 hem. )

Consequence

TEX13A
NM_031274.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -1.02

Variant links:

Genes affected

TEX13A (HGNC:11735): (testis expressed 13A) This gene is similar to a mouse gene that is expressed in the testis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

TEX13A links:

IL1RAPL2 (HGNC:5997): (interleukin 1 receptor accessory protein like 2) The protein encoded by this gene is a member of the interleukin 1 receptor family. This protein is similar to the interleukin 1 accessory proteins, and is most closely related to interleukin 1 receptor accessory protein-like 1 (IL1RAPL1). This gene and IL1RAPL1 are located at a region on chromosome X that is associated with X-linked non-syndromic cognitive disability. [provided by RefSeq, Jul 2008]

IL1RAPL2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.02958256).

BS2

High Hemizygotes in GnomAdExome4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX13A	NM_031274.5 linkuse as main transcript	c.86C>T	p.Thr29Met	missense_variant	2/3	ENST00000600991.6	NP_112564.1	Q9BXU3
IL1RAPL2	NM_017416.2 linkuse as main transcript	c.357-13506G>A		intron_variant		ENST00000372582.6	NP_059112.1	Q9NP60
TEX13A	NM_001291277.2 linkuse as main transcript	c.86C>T	p.Thr29Met	missense_variant	2/3		NP_001278206.1	Q9BXU3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
TEX13A	ENST00000600991.6 linkuse as main transcript	c.86C>T	p.Thr29Met	missense_variant	2/3	1	NM_031274.5	ENSP00000471604.2	Q9BXU3
TEX13A	ENST00000609007.3 linkuse as main transcript	c.86C>T	p.Thr29Met	missense_variant	2/3	1		ENSP00000477478.2	Q9BXU3
IL1RAPL2	ENST00000372582.6 linkuse as main transcript	c.357-13506G>A		intron_variant		1	NM_017416.2	ENSP00000361663.1	Q9NP60

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.0000824

AC:

AN:

182016

Hom.:

AF XY:

0.0000901

AC XY:

AN XY:

66580

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.000439

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.000668

GnomAD4 exome

AF:

0.0000164

AC:

AN:

1096701

Hom.:

Cov.:

AF XY:

0.0000166

AC XY:

AN XY:

362173

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.000398

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000185

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.0000652

GnomAD4 genome

Cov.:

Bravo

AF:

0.0000113

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000149

AC:

ExAC

AF:

0.0000824

AC:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 04, 2024

The c.86C>T (p.T29M) alteration is located in exon 2 (coding exon 1) of the TEX13A gene. This alteration results from a C to T substitution at nucleotide position 86, causing the threonine (T) at amino acid position 29 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.011

DANN

Benign

0.85

DEOGEN2

Benign

0.037

T;T

FATHMM_MKL

Benign

0.0057

LIST_S2

Benign

0.21

.;T

M_CAP

Benign

0.0017

MetaRNN

Benign

0.030

T;T

MetaSVM

Benign

-1.0

PrimateAI

Benign

0.32

Sift4G

Benign

0.15

T;T

Polyphen

0.63

P;P

Vest4

0.20

MVP

0.014

ClinPred

0.036

GERP RS

-5.6

Varity_R

0.024

gMVP

0.087

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

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