GJC1
Basic information
Region (hg38): 17:44798448-44830816
Previous symbols: [ "GJA7" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (28 variants)
- not_provided (2 variants)
- EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the GJC1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005497.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 28 | 29 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 28 | 1 | 2 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| GJC1 | protein_coding | protein_coding | ENST00000426548 | 1 | 32369 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.988 | 0.0120 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.07 | 135 | 222 | 0.608 | 0.0000130 | 2626 |
| Missense in Polyphen | 35 | 94.384 | 0.37083 | 1140 | ||
| Synonymous | 0.313 | 81 | 84.7 | 0.957 | 0.00000485 | 764 |
| Loss of Function | 3.38 | 0 | 13.3 | 0.00 | 8.33e-7 | 150 |
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) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: One gap junction consists of a cluster of closely packed pairs of transmembrane channels, the connexons, through which materials of low MW diffuse from one cell to a neighboring cell.;
- Pathway
- Calcium Regulation in the Cardiac Cell;Electric Transmission Across Gap Junctions;Transmission across Electrical Synapses ;Neuronal System
(Consensus)
Recessive Scores
- pRec
- 0.175
Intolerance Scores
- loftool
- 0.0404
- rvis_EVS
- -0.12
- rvis_percentile_EVS
- 44.89
Haploinsufficiency Scores
- pHI
- 0.428
- hipred
- Y
- hipred_score
- 0.817
- ghis
- 0.538
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.373
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Gjc1
- 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); vision/eye phenotype; embryo phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); muscle phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- cx43.4
- Affected structure
- pancreatic bud
- Phenotype tag
- abnormal
- Phenotype quality
- mislocalised radially
Gene ontology
- Biological process
- vasculogenesis;muscle contraction;cell-cell junction assembly;chemical synaptic transmission;visual perception;gap junction assembly;ion transmembrane transport;cell development;cardiac muscle tissue development;atrial cardiac muscle cell action potential;SA node cell to atrial cardiac muscle cell communication by electrical coupling;AV node cell to bundle of His cell communication by electrical coupling
- Cellular component
- endoplasmic reticulum membrane;plasma membrane;gap junction;connexin complex;intercalated disc;integral component of membrane
- Molecular function
- ion channel activity;gap junction channel activity involved in SA node cell-atrial cardiac muscle cell electrical coupling;gap junction channel activity involved in AV node cell-bundle of His cell electrical coupling