chrX-28587759-G-GT

Variant names:

• chrX-28587759-G-GT
• rs779869307
• NM_014271.4:c.-302dupT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_014271.4(IL1RAPL1):​c.-302dupT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: 𝑓 0.0035 (2 hom., 76 hem., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom. 0 hem.)
  • Failed GnomAD Quality Control
• Consequence: IL1RAPL1 NM_014271.4 5_prime_UTR
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.0760

Genes affected

IL1RAPL1 (HGNC:5996): (interleukin 1 receptor accessory protein like 1) The protein encoded by this gene is a member of the interleukin 1 receptor family and is similar to the interleukin 1 accessory proteins. This protein has an N-terminal signal peptide, three extracellular immunoglobulin Ig-like domains, a transmembrane domain, an intracellular Toll/IL-1R domain, and a long C-terminal tail which interacts with multiple signalling molecules. This gene is located at a region on chromosome X that is associated with a non-syndromic form of X-linked intellectual disability. Deletions and mutations in this gene were found in patients with intellectual disability. This gene is expressed at a high level in post-natal brain structures involved in the hippocampal memory system, which suggests a specialized role in the physiological processes underlying memory and learning abilities, and plays a role in synapse formation and stabilization. [provided by RefSeq, Jul 2017]

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 2 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL1RAPL1	NM_014271.4	c.-302dupT		5_prime_UTR_variant	Exon 1 of 11	ENST00000378993.6	NP_055086.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IL1RAPL1	ENST00000378993	c.-302dupT		5_prime_UTR_variant	Exon 1 of 11	1	NM_014271.4	ENSP00000368278.1

Frequencies

GnomAD3 genomes AF: 0.00354 AC: 361 AN: 101899 Hom.: 2 Cov.: 0 AF XY: 0.00292 AC XY: 76 AN XY: 26001

Gnomad AFR AF: 0.0104

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00171

Gnomad ASJ AF: 0.00199

Gnomad EAS AF: 0.000309

Gnomad SAS AF: 0.00177

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00444

Gnomad NFE AF: 0.000837

Gnomad OTH AF: 0.00147

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.00354 AC: 361 AN: 101903 Hom.: 2 Cov.: 0 AF XY: 0.00292 AC XY: 76 AN XY: 26017

Gnomad4 AFR AF: 0.0104

Gnomad4 AMR AF: 0.00171

Gnomad4 ASJ AF: 0.00199

Gnomad4 EAS AF: 0.000310

Gnomad4 SAS AF: 0.00179

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000837

Gnomad4 OTH AF: 0.00145

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Non-syndromic X-linked intellectual disability Uncertain:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

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: rs779869307; hg19: chrX-28605876;