ORAI2
Basic information
Region (hg38): 7:102433106-102456825
Previous symbols: [ "C7orf19", "TMEM142B" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ORAI2 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 10 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 1 | 1 |
Variants in ORAI2
This is a list of pathogenic ClinVar variants found in the ORAI2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-102438984-G-A | not specified | Uncertain significance (Dec 28, 2023) | ||
| 7-102439005-C-T | not specified | Likely benign (May 11, 2022) | ||
| 7-102439014-G-A | not specified | Uncertain significance (Sep 17, 2021) | ||
| 7-102439020-A-G | not specified | Uncertain significance (Oct 13, 2023) | ||
| 7-102439030-A-G | not specified | Uncertain significance (Dec 01, 2022) | ||
| 7-102439157-C-T | Benign (Aug 02, 2017) | |||
| 7-102446562-C-G | not specified | Uncertain significance (May 13, 2024) | ||
| 7-102446813-G-A | not specified | Uncertain significance (Jan 22, 2024) | ||
| 7-102446822-C-T | not specified | Uncertain significance (Apr 11, 2023) | ||
| 7-102446841-C-A | not specified | Uncertain significance (Feb 27, 2023) | ||
| 7-102446862-C-T | not specified | Uncertain significance (Oct 12, 2021) | ||
| 7-102446865-G-A | not specified | Uncertain significance (Jan 24, 2023) | ||
| 7-102446946-G-A | not specified | Uncertain significance (Sep 01, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ORAI2 | protein_coding | protein_coding | ENST00000356387 | 2 | 23716 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.205 | 0.757 | 125717 | 0 | 4 | 125721 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.45 | 114 | 167 | 0.683 | 0.0000112 | 1635 |
| Missense in Polyphen | 49 | 87.368 | 0.56085 | 914 | ||
| Synonymous | -0.220 | 81 | 78.5 | 1.03 | 0.00000574 | 550 |
| Loss of Function | 1.72 | 2 | 6.87 | 0.291 | 2.98e-7 | 70 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000377 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Ca(2+) release-activated Ca(2+)-like (CRAC-like) channel subunit which mediates Ca(2+) influx and increase in Ca(2+)- selective current by synergy with the Ca(2+) sensor, STIM1. {ECO:0000269|PubMed:16807233, ECO:0000269|PubMed:17452328}.;
- Pathway
- Calcium signaling pathway - Homo sapiens (human);Antigen activates B Cell Receptor (BCR) leading to generation of second messengers;Signaling by the B Cell Receptor (BCR);Immune System;Adaptive Immune System;Ion homeostasis;Cardiac conduction;Muscle contraction;Hemostasis;Elevation of cytosolic Ca2+ levels;Platelet calcium homeostasis;Platelet homeostasis
(Consensus)
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- loftool
- 0.110
- rvis_EVS
- -0.29
- rvis_percentile_EVS
- 32.94
Haploinsufficiency Scores
- pHI
- 0.323
- hipred
- Y
- hipred_score
- 0.662
- ghis
- 0.651
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.956
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Orai2
- Phenotype
- hematopoietic system phenotype; immune system phenotype;
Gene ontology
- Biological process
- store-operated calcium entry;calcium ion transmembrane transport
- Cellular component
- membrane;integral component of membrane;growth cone
- Molecular function
- protein binding;store-operated calcium channel activity