CA5A

carbonic anhydrase 5A, the group of Carbonic anhydrases

Basic information

Region (hg38): 16:87881546-87936580

Previous symbols: [ "CA5" ]

Links

ENSG00000174990

∙ NCBI:763 ∙ OMIM:114761 ∙ HGNC:1377 ∙ Uniprot:P35218 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

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: CGD

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 ClinVar and linked to the CA5A gene.

Hyperammonemic_encephalopathy_due_to_carbonic_anhydrase_VA_deficiency (153 variants)
Inborn_genetic_diseases (58 variants)
not_provided (33 variants)
CA5A-related_disorder (15 variants)
not_specified (8 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. These statistics are base on transcript: NM_000001739.2. 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 clinvar	1 clinvar	49 clinvar	2 clinvar	53
missense		2 clinvar	96 clinvar	13 clinvar	2 clinvar	113
nonsense	2 clinvar	1 clinvar	1 clinvar			4
start loss						0
frameshift	1 clinvar	1 clinvar				2
splice donor/acceptor (+/-2bp)	2 clinvar	3 clinvar				5
Total	5	8	98	62	4

Highest pathogenic variant AF is 0.000171641

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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