rs56000396

Variant names:

• chrX-105219594-C-CA
• rs56000396
• NM_031274.5:c.599dupT

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_031274.5(TEX13A):​c.599dupT​(p.Glu201GlyfsTer53) 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.98
• Publications: 9 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031274.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX13A	NM_031274.5	MANE Select	c.599dupT	p.Glu201GlyfsTer53	frameshift	Exon 3 of 3	NP_112564.1
	IL1RAPL2	NM_017416.2	MANE Select	c.357-14223dupA		intron	N/A	NP_059112.1
	TEX13A	NM_001291277.2		c.599dupT	p.Glu201GlyfsTer53	frameshift	Exon 3 of 3	NP_001278206.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TEX13A	ENST00000600991.6	TSL:1 MANE Select	c.599dupT	p.Glu201GlyfsTer53	frameshift	Exon 3 of 3	ENSP00000471604.2
	TEX13A	ENST00000609007.3	TSL:1	c.599dupT	p.Glu201GlyfsTer53	frameshift	Exon 3 of 3	ENSP00000477478.2
	IL1RAPL2	ENST00000372582.6	TSL:1 MANE Select	c.357-14223dupA		intron	N/A	ENSP00000361663.1

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 22

Alfa AF: 0.000221 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-4.0

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

Other links and lift over

dbSNP: rs56000396; hg19: chrX-104464276;