chrX-118766850-T-A

Variant names:

• chrX-118766850-T-A
• rs1340985667
• NM_001560.3:c.883T>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001560.3(IL13RA1):​c.883T>A​(p.Ser295Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/20 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: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: IL13RA1 NM_001560.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

Genes affected

IL13RA1 (HGNC:5974): (interleukin 13 receptor subunit alpha 1) The protein encoded by this gene is a subunit of the interleukin 13 receptor. This subunit forms a receptor complex with IL4 receptor alpha, a subunit shared by IL13 and IL4 receptors. This subunit serves as a primary IL13-binding subunit of the IL13 receptor, and may also be a component of IL4 receptors. This protein has been shown to bind tyrosine kinase TYK2, and thus may mediate the signaling processes that lead to the activation of JAK1, STAT3 and STAT6 induced by IL13 and IL4. [provided by RefSeq, Jul 2008]

ACMG classification

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=0.07643843).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL13RA1	NM_001560.3	c.883T>A	p.Ser295Thr	missense_variant	Exon 8 of 11	ENST00000371666.8	NP_001551.1
IL13RA1	XM_047442096.1	c.883T>A	p.Ser295Thr	missense_variant	Exon 8 of 11		XP_047298052.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL13RA1	ENST00000371666.8	c.883T>A	p.Ser295Thr	missense_variant	Exon 8 of 11	1	NM_001560.3	ENSP00000360730.3
IL13RA1	ENST00000652600.1	c.877T>A	p.Ser293Thr	missense_variant	Exon 9 of 12			ENSP00000498980.1
IL13RA1	ENST00000481868.1	n.576T>A		non_coding_transcript_exon_variant	Exon 6 of 6	3

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 932430 Hom.: 0 Cov.: 16 AF XY: 0.00 AC XY: 0 AN XY: 267368

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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 23

Bravo AF: 0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.077
BayesDel_addAF	Benign	-0.35	T
BayesDel_noAF	Benign	-0.73
CADD	Benign	2.1
DANN	Benign	0.61
DEOGEN2	Benign	0.15	T
FATHMM_MKL	Benign	0.0025	N
LIST_S2	Benign	0.44	T
M_CAP	Benign	0.025	T
MetaRNN	Benign	0.076	T
MetaSVM	Benign	-0.83	T
MutationAssessor	Benign	-0.20	N
PrimateAI	Benign	0.36	T
PROVEAN	Benign	-0.56	N
REVEL	Benign	0.22
Sift	Benign	0.47	T
Sift4G	Benign	0.98	T
Polyphen		0.0	B
Vest4		0.068
MutPred		0.51		Gain of glycosylation at S295 (P = 0.101);
MVP		0.29
MPC		0.15
ClinPred		0.048	T
GERP RS		1.4
Varity_R		0.42
gMVP		0.36

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

Other links and lift over

dbSNP: rs1340985667; hg19: chrX-117900813;