X-105219970-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_031274.5(TEX13A):​c.428G>C​(p.Arg143Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000887 in 112,750 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 10/15 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R143K) has been classified as Uncertain significance.

Frequency

Genomes: š‘“ 0.0000089 ( 0 hom., 0 hem., cov: 23)
Exomes š‘“: 9.2e-7 ( 0 hom. 1 hem. )
Failed GnomAD Quality Control

Consequence

TEX13A
NM_031274.5 missense

Scores

2
11

Clinical Significance

Not reported in ClinVar

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]
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

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=0.24853921).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
TEX13ANM_031274.5 linkc.428G>C p.Arg143Thr missense_variant Exon 2 of 3 ENST00000600991.6 NP_112564.1 Q9BXU3
IL1RAPL2NM_017416.2 linkc.357-13848C>G intron_variant Intron 3 of 10 ENST00000372582.6 NP_059112.1 Q9NP60
TEX13ANM_001291277.2 linkc.428G>C p.Arg143Thr missense_variant Exon 2 of 3 NP_001278206.1 Q9BXU3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
TEX13AENST00000600991.6 linkc.428G>C p.Arg143Thr missense_variant Exon 2 of 3 1 NM_031274.5 ENSP00000471604.2 Q9BXU3
TEX13AENST00000609007.3 linkc.428G>C p.Arg143Thr missense_variant Exon 2 of 3 1 ENSP00000477478.2 Q9BXU3
IL1RAPL2ENST00000372582.6 linkc.357-13848C>G intron_variant Intron 3 of 10 1 NM_017416.2 ENSP00000361663.1 Q9NP60

Frequencies

GnomAD3 genomes
AF:
0.00000887
AC:
1
AN:
112750
Hom.:
0
Cov.:
23
AF XY:
0.00
AC XY:
0
AN XY:
34896
show subpopulations
Gnomad AFR
AF:
0.0000322
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
9.21e-7
AC:
1
AN:
1085689
Hom.:
0
Cov.:
31
AF XY:
0.00000282
AC XY:
1
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:
0.0000333
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.00000887
AC:
1
AN:
112750
Hom.:
0
Cov.:
23
AF XY:
0.00
AC XY:
0
AN XY:
34896
show subpopulations
Gnomad4 AFR
AF:
0.0000322
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.35
BayesDel_addAF
Benign
-0.27
T
BayesDel_noAF
Benign
-0.62
CADD
Benign
9.9
DANN
Benign
0.88
DEOGEN2
Benign
0.37
T;T
FATHMM_MKL
Benign
0.020
N
LIST_S2
Benign
0.58
.;T
M_CAP
Benign
0.0033
T
MetaRNN
Benign
0.25
T;T
MetaSVM
Benign
-1.0
T
PrimateAI
Benign
0.36
T
Sift4G
Uncertain
0.022
D;D
Polyphen
0.84
P;P
Vest4
0.51
MutPred
0.28
Gain of phosphorylation at R143 (P = 0.0441);Gain of phosphorylation at R143 (P = 0.0441);
MVP
0.055
ClinPred
0.22
T
GERP RS
-0.073
Varity_R
0.068
gMVP
0.22

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.

Other links and lift over

dbSNP: rs782792744; hg19: chrX-104464654; API