CANX
calnexin
Basic information
Region (hg38): 5:179678628-179731641
Links
Phenotypes
GenCC
Source:
No genCC data.
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 CANX 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 | 0 | |||||
| missense | 23 | 24 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 16 | 16 | ||||
| Total | 0 | 0 | 39 | 1 | 0 |
Variants in CANX
This is a list of pathogenic ClinVar variants found in the CANX region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-179678722-A-G | not specified | Uncertain significance (Jul 29, 2023) | ||
| 5-179678730-C-T | not specified | Uncertain significance (Aug 22, 2023) | ||
| 5-179678731-A-T | not specified | Uncertain significance (Jul 25, 2023) | ||
| 5-179678749-T-A | not specified | Uncertain significance (May 26, 2022) | ||
| 5-179678771-G-C | not specified | Uncertain significance (May 27, 2022) | ||
| 5-179678891-T-G | not specified | Uncertain significance (Sep 06, 2022) | ||
| 5-179678925-G-C | not specified | Uncertain significance (Jan 04, 2022) | ||
| 5-179678962-C-T | not specified | Uncertain significance (May 30, 2024) | ||
| 5-179678983-T-C | not specified | Uncertain significance (Mar 12, 2024) | ||
| 5-179679089-T-C | not specified | Uncertain significance (Oct 13, 2023) | ||
| 5-179679095-A-C | not specified | Uncertain significance (Aug 02, 2021) | ||
| 5-179679102-G-T | not specified | Uncertain significance (Dec 13, 2021) | ||
| 5-179679110-G-A | not specified | Uncertain significance (Oct 27, 2023) | ||
| 5-179679115-G-A | not specified | Uncertain significance (Jun 24, 2022) | ||
| 5-179679170-T-A | not specified | Uncertain significance (Jan 19, 2024) | ||
| 5-179679226-C-T | not specified | Uncertain significance (Apr 18, 2023) | ||
| 5-179679254-C-T | not specified | Uncertain significance (Sep 13, 2023) | ||
| 5-179705739-G-T | not specified | Uncertain significance (Jun 18, 2024) | ||
| 5-179705768-T-G | not specified | Uncertain significance (Dec 01, 2022) | ||
| 5-179705781-G-C | not specified | Uncertain significance (Aug 17, 2022) | ||
| 5-179705827-C-T | not specified | Uncertain significance (Nov 09, 2023) | ||
| 5-179706327-T-G | not specified | Uncertain significance (Dec 28, 2022) | ||
| 5-179707166-G-A | not specified | Uncertain significance (Mar 25, 2024) | ||
| 5-179708353-T-A | not specified | Uncertain significance (Nov 15, 2021) | ||
| 5-179708359-A-G | not specified | Uncertain significance (Sep 22, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CANX | protein_coding | protein_coding | ENST00000247461 | 14 | 52298 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.866 | 0.134 | 125733 | 0 | 15 | 125748 | 0.0000596 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.58 | 238 | 317 | 0.750 | 0.0000154 | 3947 |
| Missense in Polyphen | 51 | 123.55 | 0.41278 | 1590 | ||
| Synonymous | -0.347 | 115 | 110 | 1.04 | 0.00000590 | 1049 |
| Loss of Function | 4.36 | 6 | 33.0 | 0.182 | 0.00000163 | 405 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000981 | 0.0000905 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000633 | 0.0000615 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.000136 | 0.000131 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Calcium-binding protein that interacts with newly synthesized glycoproteins in the endoplasmic reticulum. It may act in assisting protein assembly and/or in the retention within the ER of unassembled protein subunits. It seems to play a major role in the quality control apparatus of the ER by the retention of incorrectly folded proteins. Associated with partial T-cell antigen receptor complexes that escape the ER of immature thymocytes, it may function as a signaling complex regulating thymocyte maturation. Additionally it may play a role in receptor- mediated endocytosis at the synapse.;
- Pathway
- Antigen processing and presentation - Homo sapiens (human);Thyroid hormone synthesis - Homo sapiens (human);Phagosome - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);HTLV-I infection - Homo sapiens (human);Interleukin-12 family signaling;Disease;Signaling by Interleukins;Cytokine Signaling in Immune system;Calnexin/calreticulin cycle;Post-translational protein modification;Assembly of Viral Components at the Budding Site;Metabolism of proteins;Virus Assembly and Release;Influenza Life Cycle;Influenza Infection;MHC class II antigen presentation;Infectious disease;Immune System;Adaptive Immune System;Class I MHC mediated antigen processing & presentation;Asparagine N-linked glycosylation;Interleukin-27 signaling;TSH;N-glycan trimming in the ER and Calnexin/Calreticulin cycle;Antigen Presentation: Folding, assembly and peptide loading of class I MHC
(Consensus)
Recessive Scores
- pRec
- 0.895
Intolerance Scores
- loftool
- 0.700
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.91
Haploinsufficiency Scores
- pHI
- 0.784
- hipred
- Y
- hipred_score
- 0.745
- ghis
- 0.641
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.992
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Canx
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Zebrafish Information Network
- Gene name
- canx
- Affected structure
- neuromast hair cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- antigen processing and presentation of peptide antigen via MHC class I;protein folding;aging;protein secretion;antigen processing and presentation of exogenous peptide antigen via MHC class II;protein folding in endoplasmic reticulum;synaptic vesicle endocytosis;chaperone-mediated protein folding;interleukin-27-mediated signaling pathway;interleukin-35-mediated signaling pathway;clathrin-dependent endocytosis
- Cellular component
- endoplasmic reticulum;endoplasmic reticulum lumen;endoplasmic reticulum membrane;smooth endoplasmic reticulum;rough endoplasmic reticulum;ribosome;membrane;axon;dendrite cytoplasm;melanosome;neuronal cell body;dendritic spine;myelin sheath;mitochondria-associated endoplasmic reticulum membrane;endoplasmic reticulum quality control compartment;extracellular exosome;integral component of lumenal side of endoplasmic reticulum membrane;glutamatergic synapse;integral component of postsynaptic membrane;integral component of presynaptic active zone membrane
- Molecular function
- RNA binding;calcium ion binding;protein binding;carbohydrate binding;apolipoprotein binding;ionotropic glutamate receptor binding;unfolded protein binding