CA1

carbonic anhydrase 1, the group of Carbonic anhydrases

Basic information

Region (hg38): 8:85327608-85379014

Links

ENSG00000133742 ∙ NCBI:759 ∙ OMIM:114800 ∙ HGNC:1368 ∙ Uniprot:P00915 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CA1 gene.

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.

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					1	1
missense			13		3	16
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	4

Variants in CA1

This is a list of pathogenic ClinVar variants found in the CA1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
8-85328576-A-G		not specified	Uncertain significance (Dec 23, 2023)
8-85328586-C-G		Carbonic anhydrase I, Guam	Pathogenic (Jan 01, 1981)
8-85328606-C-T		Carbonic anhydrase I deficiency	Pathogenic (Jul 29, 1977)
8-85328627-A-G		not specified	Uncertain significance (Aug 21, 2023)
8-85328652-A-T		not specified	Uncertain significance (Jun 29, 2022)
8-85328670-G-T		not specified	Uncertain significance (Jul 14, 2021)
8-85329713-C-G		not specified	Uncertain significance (Jun 28, 2023)
8-85329771-G-A			Benign (Jul 31, 2018)
8-85329808-T-C		not specified	Uncertain significance (Jul 15, 2021)
8-85332503-G-A			Benign (Jul 27, 2018)
8-85333547-G-A			Benign (Dec 11, 2017)
8-85333605-AGT-A		Renal tubular acidosis;Rickets;Metabolic acidosis	Uncertain significance (Nov 09, 2019)
8-85333615-G-A			Benign (Nov 08, 2017)
8-85336947-C-T		not specified	Uncertain significance (Jul 09, 2021)
8-85336985-C-T		not specified	Uncertain significance (Jan 19, 2022)
8-85336992-C-T		not specified	Uncertain significance (Aug 04, 2023)
8-85338340-A-T		not specified	Uncertain significance (Jun 22, 2023)
8-85338398-G-C		not specified	Uncertain significance (Dec 22, 2023)
8-85338422-G-A		not specified	Uncertain significance (Feb 13, 2024)
8-85338423-G-A		not specified	Uncertain significance (Jul 27, 2021)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• 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

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