chr12-121626888-G-GCCGCCGCCGCAGCGGGGACGGGGAGCCCCCGGGGGCC
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The ENST00000617316.2(ORAI1):c.141_142insCCGCCGCCGCAGCGGGGACGGGGAGCCCCCGGGGGCC(p.Ser48fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Consequence
ORAI1
ENST00000617316.2 frameshift
ENST00000617316.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.140
Genes affected
ORAI1 (HGNC:25896): (ORAI calcium release-activated calcium modulator 1) The protein encoded by this gene is a membrane calcium channel subunit that is activated by the calcium sensor STIM1 when calcium stores are depleted. This type of channel is the primary way for calcium influx into T-cells. Defects in this gene are a cause of immune dysfunction with T-cell inactivation due to calcium entry defect type 1 (IDTICED1). [provided by RefSeq, Sep 2011]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 12-121626888-G-GCCGCCGCCGCAGCGGGGACGGGGAGCCCCCGGGGGCC is Pathogenic according to our data. Variant chr12-121626888-G-GCCGCCGCCGCAGCGGGGACGGGGAGCCCCCGGGGGCC is described in ClinVar as [Pathogenic]. Clinvar id is 470188.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ORAI1 | NR_186857.1 | n.359_360insCCGCCGCCGCAGCGGGGACGGGGAGCCCCCGGGGGCC | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ORAI1 | ENST00000617316.2 | c.141_142insCCGCCGCCGCAGCGGGGACGGGGAGCCCCCGGGGGCC | p.Ser48fs | frameshift_variant | 2/3 | 1 | ENSP00000482568.2 | |||
ORAI1 | ENST00000611718.1 | n.73_74insCCGCCGCCGCAGCGGGGACGGGGAGCCCCCGGGGGCC | non_coding_transcript_exon_variant | 1/2 | 5 | |||||
ORAI1 | ENST00000646827.1 | n.339_340insCCGCCGCCGCAGCGGGGACGGGGAGCCCCCGGGGGCC | non_coding_transcript_exon_variant | 1/2 | ||||||
ORAI1 | ENST00000698901.1 | n.380_381insCCGCCGCCGCAGCGGGGACGGGGAGCCCCCGGGGGCC | non_coding_transcript_exon_variant | 1/2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Cov.: 34
GnomAD4 exome
Cov.:
34
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Combined immunodeficiency due to ORAI1 deficiency Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 21, 2017 | This sequence change results in a premature translational stop signal in the ORAI1 gene (p.Ser48Glnfs*52). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 254 amino acids (>80%) of the ORAI1 protein. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with an ORAI1-related disease. Loss-of function variants in ORAI1 are known to be causative of autosomal recessive ORAI1 deficiency. Truncating variants downstream of this variant (p.Ala88serfs*25, p.His165Profs*2, p.Arg268*) have been reported in homozygous and compound heterozygous individuals with ORAI1 deficiency and determined to be pathogenic (PMID: 26070885, 20004786, 27063589). This suggests that deletion of the C-terminal region of the ORAI1 protein is causative of disease. In summary, this is a novel insertion that leads to the disruption of most of the ORAI1 protein sequence, and truncating variants downstream from this variant have been shown to be deleterious. Therefore, it has been classified as Pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at