CA1
Basic information
Region (hg38): 8:85327608-85379014
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (25 variants)
- not_provided (4 variants)
- Rickets (1 variants)
- Carbonic_anhydrase_I,_Guam (1 variants)
- Metabolic_acidosis (1 variants)
- Renal_tubular_acidosis (1 variants)
- Carbonic_anhydrase_I_deficiency (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CA1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001128831.4. 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 | 1 | |||||
missense | 24 | 30 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 2 | 0 | 25 | 1 | 4 |
Highest pathogenic variant AF is 0.0000086865
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CA1 | protein_coding | protein_coding | ENST00000523953 | 7 | 51407 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
4.75e-11 | 0.0300 | 125665 | 0 | 55 | 125720 | 0.000219 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.210 | 143 | 136 | 1.05 | 0.00000660 | 1711 |
Missense in 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 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000125 | 0.000125 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000929 | 0.000925 |
Finnish | 0.000375 | 0.000370 |
European (Non-Finnish) | 0.0000918 | 0.0000879 |
Middle Eastern | 0.000929 | 0.000925 |
South Asian | 0.000545 | 0.000490 |
Other | 0.000164 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Reversible hydration of carbon dioxide. Can hydrates cyanamide to urea. {ECO:0000269|PubMed:10550681}.;
- Pathway
- Nitrogen metabolism - Homo sapiens (human);Pantoprazole Action Pathway;Rabeprazole Action Pathway;Esomeprazole Action Pathway;Omeprazole Action Pathway;Lansoprazole Action Pathway;Gastric Acid Production;Nizatidine Action Pathway;Cimetidine Action Pathway;Famotidine Action Pathway;Ranitidine Action Pathway;Betazole Action Pathway;Roxatidine acetate Action Pathway;Metiamide Action Pathway;Pirenzepine Action Pathway;Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;Metabolism;O2/CO2 exchange in erythrocytes;Transport of small molecules;Erythrocytes take up oxygen and release carbon dioxide;Erythrocytes take up carbon dioxide and release oxygen;C-MYB transcription factor network;Reversible hydration of carbon dioxide
(Consensus)
Recessive Scores
- pRec
- 0.164
Intolerance Scores
- loftool
- 0.795
- rvis_EVS
- 0.57
- rvis_percentile_EVS
- 81.99
Haploinsufficiency Scores
- pHI
- 0.395
- hipred
- N
- hipred_score
- 0.170
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.845
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Car1
- Phenotype
Gene ontology
- Biological process
- one-carbon metabolic process;bicarbonate transport;interleukin-12-mediated signaling pathway
- Cellular component
- cytosol;extracellular exosome
- Molecular function
- arylesterase activity;carbonate dehydratase activity;protein binding;zinc ion binding;hydro-lyase activity