Variant X-105219970-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_031274.5(TEX13A):c.428G>A(p.Arg143Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000368 in 1,085,689 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 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. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 23)

Exomes 𝑓: 0.0000037 ( 0 hom. 1 hem. )

Consequence

TEX13A
NM_031274.5 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.933

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 Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.06557834).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TEX13A	NM_031274.5 linkuse as main transcript	c.428G>A	p.Arg143Lys	missense_variant	2/3	ENST00000600991.6	NP_112564.1	Q9BXU3
IL1RAPL2	NM_017416.2 linkuse as main transcript	c.357-13848C>T		intron_variant		ENST00000372582.6	NP_059112.1	Q9NP60
TEX13A	NM_001291277.2 linkuse as main transcript	c.428G>A	p.Arg143Lys	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.428G>A	p.Arg143Lys	missense_variant	2/3	1	NM_031274.5	ENSP00000471604.2	Q9BXU3
TEX13A	ENST00000609007.3 linkuse as main transcript	c.428G>A	p.Arg143Lys	missense_variant	2/3	1		ENSP00000477478.2	Q9BXU3
IL1RAPL2	ENST00000372582.6 linkuse as main transcript	c.357-13848C>T		intron_variant		1	NM_017416.2	ENSP00000361663.1	Q9NP60

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000590

AC:

AN:

169567

Hom.:

AF XY:

0.0000174

AC XY:

AN XY:

57549

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

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:

0.0000130

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000368

AC:

AN:

1085689

Hom.:

Cov.:

AF XY:

0.00000282

AC XY:

AN XY:

354375

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000479

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Bravo

AF:

0.00000378

ExAC

AF:

0.00000826

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

Apr 23, 2024

The c.428G>A (p.R143K) alteration is located in exon 2 (coding exon 1) of the TEX13A gene. This alteration results from a G to A substitution at nucleotide position 428, causing the arginine (R) at amino acid position 143 to be replaced by a lysine (K). 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

0.16

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.4

DANN

Benign

0.78

DEOGEN2

Benign

0.12

T;T

FATHMM_MKL

Benign

0.021

LIST_S2

Benign

0.39

.;T

M_CAP

Benign

0.0025

MetaRNN

Benign

0.066

T;T

MetaSVM

Benign

-1.0

PrimateAI

Benign

0.37

Sift4G

Benign

0.11

T;T

Polyphen

0.078

B;B

Vest4

0.36

MutPred

0.33

Gain of ubiquitination at R143 (P = 0.0085);Gain of ubiquitination at R143 (P = 0.0085);

MVP

0.030

ClinPred

0.031

GERP RS

-0.073

Varity_R

0.052

gMVP

0.15

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