GeneBe

rs56118606

Positions:

Variant summary

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

The NM_031274.5(TEX13A):​c.595del​(p.Asp199MetfsTer154) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 22)

Consequence

TEX13A
NM_031274.5 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.425
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 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TEX13ANM_031274.5 linkuse as main transcriptc.595del p.Asp199MetfsTer154 frameshift_variant 3/3 ENST00000600991.6 NP_112564.1
IL1RAPL2NM_017416.2 linkuse as main transcriptc.357-14217del intron_variant ENST00000372582.6 NP_059112.1
TEX13ANM_001291277.2 linkuse as main transcriptc.595del p.Asp199MetfsTer154 frameshift_variant 3/3 NP_001278206.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TEX13AENST00000600991.6 linkuse as main transcriptc.595del p.Asp199MetfsTer154 frameshift_variant 3/31 NM_031274.5 ENSP00000471604 P1
TEX13AENST00000609007.3 linkuse as main transcriptc.595del p.Asp199MetfsTer154 frameshift_variant 3/31 ENSP00000477478 P1
IL1RAPL2ENST00000372582.6 linkuse as main transcriptc.357-14217del intron_variant 1 NM_017416.2 ENSP00000361663 P1

Frequencies

GnomAD3 genomes
Cov.:
22
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs56118606; hg19: -; API