CA5A
Basic information
Region (hg38): 16:87881546-87936580
Previous symbols: [ "CA5" ]
Links
Phenotypes
GenCC
Source:
- hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency (Strong), mode of inheritance: AR
- hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency (Strong), mode of inheritance: AR
- hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency (Moderate), mode of inheritance: AR
- hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency (Supportive), mode of inheritance: AR
- hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Carbonic anhydrase VA deficiency | AR | Biochemical | Medical treatment (eg, with N-carbamyl-L-glutamate (NCG) alone or with other treatments) has been reported as resolving hyperammonemia in affected individuals | Biochemical | 24530203; 26913920 |
ClinVar
This is a list of variants' phenotypes submitted to
- Hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CA5A 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 | 39 | 43 | ||||
| missense | 78 | 87 | ||||
| nonsense | 4 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| splice region | 8 | 8 | ||||
| non coding | 12 | 17 | ||||
| Total | 2 | 3 | 79 | 57 | 11 |
Highest pathogenic variant AF is 0.0000132
Variants in CA5A
This is a list of pathogenic ClinVar variants found in the CA5A region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CA5A | protein_coding | protein_coding | ENST00000309893 | 7 | 48511 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000791 | 0.929 | 125737 | 0 | 11 | 125748 | 0.0000437 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -1.20 | 222 | 177 | 1.25 | 0.0000108 | 1952 |
| Missense in Polyphen | 72 | 63.855 | 1.1275 | 741 | ||
| Synonymous | -1.53 | 90 | 73.3 | 1.23 | 0.00000491 | 583 |
| Loss of Function | 1.65 | 9 | 16.2 | 0.556 | 7.75e-7 | 171 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000163 | 0.000163 |
| Finnish | 0.0000924 | 0.0000924 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.000163 | 0.000163 |
| South Asian | 0.0000985 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Reversible hydration of carbon dioxide. Low activity.;
- Disease
- DISEASE: Hyperammonemia due to carbonic anhydrase VA deficiency (CA5AD) [MIM:615751]: An autosomal recessive inborn error of metabolism, clinically characterized by infantile hyperammonemic encephalopathy. Metabolic abnormalities include hypoglycemia, hyperlactatemia, metabolic acidosis and respiratory alkalosis. {ECO:0000269|PubMed:24530203}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Nitrogen metabolism - Homo sapiens (human);Metabolism;Reversible hydration of carbon dioxide
(Consensus)
Recessive Scores
- pRec
- 0.109
Intolerance Scores
- loftool
- 0.482
- rvis_EVS
- 0
- rvis_percentile_EVS
- 53.85
Haploinsufficiency Scores
- pHI
- 0.112
- hipred
- N
- hipred_score
- 0.172
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.512
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Car5a
- Phenotype
- growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism 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);
Zebrafish Information Network
- Gene name
- ca5a
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- necrotic
Gene ontology
- Biological process
- bicarbonate transport
- Cellular component
- mitochondrion;mitochondrial matrix
- Molecular function
- carbonate dehydratase activity;zinc ion binding