CNIH2
cornichon family AMPA receptor auxiliary protein 2
Basic information
Region (hg38): 11:66278175-66285301
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 CNIH2 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 | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 0 | 1 |
Variants in CNIH2
This is a list of pathogenic ClinVar variants found in the CNIH2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-66278477-G-A | Benign (Dec 19, 2017) | |||
| 11-66278481-T-C | not specified | Uncertain significance (Nov 21, 2023) | ||
| 11-66282310-G-A | not specified | Uncertain significance (May 05, 2023) | ||
| 11-66282757-C-G | not specified | Uncertain significance (Sep 22, 2023) | ||
| 11-66283279-G-A | not specified | Uncertain significance (Nov 11, 2024) | ||
| 11-66284641-C-T | not specified | Uncertain significance (Sep 23, 2023) | ||
| 11-66284720-G-A | not specified | Uncertain significance (Jul 14, 2024) | ||
| 11-66284726-G-A | not specified | Uncertain significance (Jan 07, 2025) | ||
| 11-66284728-G-A | not specified | Uncertain significance (Jan 26, 2022) | ||
| 11-66284732-C-T | not specified | Uncertain significance (Sep 27, 2021) | ||
| 11-66284750-C-T | not specified | Uncertain significance (Oct 24, 2023) | ||
| 11-66284773-A-C | not specified | Uncertain significance (Sep 15, 2021) | ||
| 11-66284779-C-T | not specified | Uncertain significance (Jan 25, 2023) | ||
| 11-66284910-G-A | not specified | Uncertain significance (Dec 21, 2024) | ||
| 11-66284916-T-C | not specified | Uncertain significance (May 28, 2024) | ||
| 11-66284926-C-T | not specified | Uncertain significance (Mar 31, 2024) | ||
| 11-66284953-C-T | not specified | Uncertain significance (Mar 20, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CNIH2 | protein_coding | protein_coding | ENST00000311445 | 6 | 7112 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.952 | 0.0482 | 125672 | 0 | 2 | 125674 | 0.00000796 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.25 | 29 | 88.6 | 0.327 | 0.00000466 | 1053 |
| Missense in Polyphen | 6 | 32.092 | 0.18696 | 418 | ||
| Synonymous | 0.986 | 28 | 35.5 | 0.789 | 0.00000199 | 290 |
| Loss of Function | 2.86 | 0 | 9.53 | 0.00 | 4.13e-7 | 110 |
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) | 0.00000887 | 0.00000880 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Regulates the trafficking and gating properties of AMPA- selective glutamate receptors (AMPARs). Promotes their targeting to the cell membrane and synapses and modulates their gating properties by regulating their rates of activation, deactivation and desensitization. Blocks CACNG8-mediated resensitization of AMPA receptors. {ECO:0000269|PubMed:20805473}.;
- Pathway
- Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Cargo concentration in the ER;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport
(Consensus)
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.155
- rvis_EVS
- -0.12
- rvis_percentile_EVS
- 44.54
Haploinsufficiency Scores
- pHI
- 0.161
- hipred
- Y
- hipred_score
- 0.707
- ghis
- 0.672
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.161
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |
Mouse Genome Informatics
- Gene name
- Cnih2
- Phenotype
- normal 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);
Gene ontology
- Biological process
- endoplasmic reticulum to Golgi vesicle-mediated transport;synaptic transmission, glutamatergic;regulation of membrane potential;COPII vesicle coating;localization within membrane;regulation of postsynaptic neurotransmitter receptor activity;negative regulation of receptor localization to synapse;negative regulation of anterograde synaptic vesicle transport;regulation of NMDA receptor activity;regulation of AMPA receptor activity
- Cellular component
- Golgi membrane;endoplasmic reticulum membrane;ER to Golgi transport vesicle membrane;postsynaptic density;cell junction;dendrite;AMPA glutamate receptor complex;endoplasmic reticulum-Golgi intermediate compartment membrane;dendritic spine;dendritic shaft;postsynaptic membrane;glutamatergic synapse;integral component of postsynaptic density membrane
- Molecular function
- protein binding