CA1
protein-codingcarbonic anhydrase 1, the group of Carbonic anhydrases
Gene summary
Carbonic anhydrases (CAs) are a large family of zinc metalloenzymes that catalyze the reversible hydration of carbon dioxide. They participate in a variety of biological processes, including respiration, calcification, acid-base balance, bone resorption, and the formation of aqueous humor, cerebrospinal fluid, saliva and gastric acid. They show extensive diversity in tissue distribution and in their subcellular localization. This CA1 gene is closely linked to the CA2 and CA3 genes on chromosome 8. It encodes a cytosolic protein that is found at the highest level in erythrocytes. Allelic variants of this gene have been described in some populations. Alternative splicing and the use of alternative promoters results in multiple transcript variants. [provided by RefSeq, Nov 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~51.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CA1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001128831.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 2 | 31 | 1 | 3 | 37 | |
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 2 | 0 | 32 | 1 | 4 | 39 |
Highest pathogenic variant AF is 0.000008686502
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001122303.1 | 7 | MANE Select | |
| Ensembl | ENSP00000429798.1 | 7 | MANE Select | |
| RefSeq | NP_001122301.1 | 7 | Standard | |
| RefSeq | NP_001122302.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Nitrogen metabolism - Homo sapiens (human)
- Pantoprazole Action Pathway
- Rabeprazole Action Pathway
- Esomeprazole Action Pathway
- Omeprazole Action Pathway
Biological Process
- one-carbon metabolic process
- bicarbonate transport
- interleukin-12-mediated signaling pathway
Molecular Function
- arylesterase activity
- carbonate dehydratase activity
- protein binding
- zinc ion binding
- hydro-lyase activity
Cellular Component
- cytosol
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000523953
- Coding exons
- 7
- Length
- 51407
- Individuals with no LoFs
- 125665
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 55
- Defined
- 125720
- p
- 0.000219
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.210 | 143 | 136 | 1.05 | 0.00000660 | 1711 |
| Missense (PolyPhen) | 58 | 53.701 | 1.0801 | 693 | ||
| Synonymous | -0.563 | 55 | 49.9 | 1.10 | 0.00000256 | 492 |
| Loss of Function | -0.377 | 15 | 13.5 | 1.11 | 7.61e-7 | 142 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00013 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00093 | 0.00092 | rare |
| Finnish | 0.00037 | 0.00037 | rare |
| European (Non-Finnish) | 0.000092 | 0.000088 | rare |
| South Asian | 0.00055 | 0.00049 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Reversible hydration of carbon dioxide. Can hydrates cyanamide to urea. {ECO:0000269|PubMed:10550681}.;
Recessive Scores
- pRec
- 0.164
Intolerance Scores
- LoFtool
- 0.795
- RVIS EVS
- 0.57
- RVIS percentile EVS
- 81.99
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.845
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |