CACNG4
calcium voltage-gated channel auxiliary subunit gamma 4, the group of Calcium channel auxiliary gamma subunits
Basic information
Region (hg38): 17:66964707-67033398
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 CACNG4 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 | 17 | 17 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 17 | 0 | 0 |
Variants in CACNG4
This is a list of pathogenic ClinVar variants found in the CACNG4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-66964930-G-A | not specified | Uncertain significance (Sep 14, 2022) | ||
| 17-66965058-C-A | not specified | Uncertain significance (Jul 25, 2023) | ||
| 17-66965083-C-G | not specified | Uncertain significance (Jul 26, 2022) | ||
| 17-67018212-C-T | not specified | Uncertain significance (Feb 23, 2023) | ||
| 17-67018213-G-A | not specified | Uncertain significance (May 25, 2022) | ||
| 17-67024865-G-C | not specified | Uncertain significance (Oct 12, 2022) | ||
| 17-67024932-G-C | not specified | Uncertain significance (Jun 07, 2024) | ||
| 17-67024953-G-A | not specified | Uncertain significance (Jul 13, 2021) | ||
| 17-67024961-A-C | not specified | Uncertain significance (Feb 27, 2024) | ||
| 17-67024979-G-A | not specified | Uncertain significance (Jan 17, 2024) | ||
| 17-67030480-A-G | not specified | Uncertain significance (Apr 19, 2023) | ||
| 17-67030520-C-T | not specified | Uncertain significance (Aug 08, 2023) | ||
| 17-67030681-T-A | not specified | Uncertain significance (May 01, 2024) | ||
| 17-67030691-C-T | not specified | Uncertain significance (Jan 31, 2022) | ||
| 17-67030733-A-G | not specified | Uncertain significance (Sep 14, 2021) | ||
| 17-67030792-G-A | not specified | Uncertain significance (Aug 17, 2021) | ||
| 17-67030847-T-C | not specified | Uncertain significance (Apr 22, 2022) | ||
| 17-67030976-T-G | not specified | Uncertain significance (Dec 12, 2023) | ||
| 17-67030985-G-A | not specified | Uncertain significance (Sep 26, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CACNG4 | protein_coding | protein_coding | ENST00000262138 | 4 | 68489 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0166 | 0.962 | 125739 | 0 | 9 | 125748 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.82 | 138 | 213 | 0.648 | 0.0000134 | 2132 |
| Missense in Polyphen | 47 | 76.722 | 0.6126 | 780 | ||
| Synonymous | -0.108 | 95 | 93.7 | 1.01 | 0.00000621 | 673 |
| Loss of Function | 2.01 | 5 | 12.7 | 0.392 | 7.99e-7 | 121 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000578 | 0.0000578 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000582 | 0.0000462 |
| European (Non-Finnish) | 0.0000287 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000982 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Regulates the activity of L-type calcium channels that contain CACNA1C as pore-forming subunit (PubMed:21127204). Regulates the trafficking and gating properties of AMPA-selective glutamate receptors (AMPARs), including GRIA1 and GRIA4. Promotes their targeting to the cell membrane and synapses and modulates their gating properties by slowing their rates of activation, deactivation and desensitization and by mediating their resensitization (PubMed:21172611). {ECO:0000269|PubMed:21127204, ECO:0000269|PubMed:21172611}.;
- Pathway
- Oxytocin signaling pathway - Homo sapiens (human);Cardiac muscle contraction - Homo sapiens (human);Dilated cardiomyopathy (DCM) - Homo sapiens (human);Arrhythmogenic right ventricular cardiomyopathy (ARVC) - Homo sapiens (human);Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human);Adrenergic signaling in cardiomyocytes - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Arrhythmogenic Right Ventricular Cardiomyopathy;MAPK Signaling Pathway;Developmental Biology;GPCR Dopamine D1like receptor;Neuronal System;Phase 0 - rapid depolarisation;Phase 2 - plateau phase;Cardiac conduction;Muscle contraction;Presynaptic depolarization and calcium channel opening;Trafficking of AMPA receptors;Glutamate binding, activation of AMPA receptors and synaptic plasticity;Neurotransmitter receptors and postsynaptic signal transmission;Transmission across Chemical Synapses;LGI-ADAM interactions
(Consensus)
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- loftool
- 0.198
- rvis_EVS
- -0.18
- rvis_percentile_EVS
- 40.16
Haploinsufficiency Scores
- pHI
- 0.663
- hipred
- Y
- hipred_score
- 0.853
- ghis
- 0.553
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.345
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cacng4
- Phenotype
- growth/size/body region 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); normal 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- transmission of nerve impulse;response to cocaine;membrane depolarization;positive regulation of synaptic transmission, glutamatergic;calcium ion transmembrane transport;neurotransmitter receptor transport, postsynaptic endosome to lysosome;regulation of postsynaptic neurotransmitter receptor activity;postsynaptic neurotransmitter receptor diffusion trapping;neurotransmitter receptor internalization;regulation of AMPA receptor activity;positive regulation of AMPA receptor activity
- Cellular component
- plasma membrane;integral component of plasma membrane;cell surface;endocytic vesicle membrane;AMPA glutamate receptor complex;somatodendritic compartment;cell body;postsynaptic density membrane;glutamatergic synapse;integral component of postsynaptic density membrane;L-type voltage-gated calcium channel complex
- Molecular function
- voltage-gated calcium channel activity;calcium channel regulator activity;calcium channel activity;channel regulator activity;ionotropic glutamate receptor binding