CA3

carbonic anhydrase 3, the group of Carbonic anhydrases

Basic information

Region (hg38): 8:85373435-85449040

Links

ENSG00000164879 ∙ NCBI:761 ∙ OMIM:114750 ∙ HGNC:1374 ∙ Uniprot:P07451 ∙ 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 CA3 gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CA3 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						0
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in CA3

This is a list of pathogenic ClinVar variants found in the CA3 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-85438937-C-T		not specified	Uncertain significance (Dec 27, 2022)
8-85439862-A-G		not specified	Uncertain significance (Jan 03, 2022)
8-85442084-G-A		not specified	Uncertain significance (Mar 21, 2023)
8-85442184-C-A		not specified	Uncertain significance (Dec 01, 2022)
8-85446197-G-A		not specified	Uncertain significance (Aug 04, 2023)
8-85448118-A-G		not specified	Uncertain significance (Dec 03, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CA3	protein_coding	protein_coding	ENST00000285381	7	75605

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00173	0.975	125726	0	22	125748	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.555	133	152	0.874	0.00000857	1705
Missense in Polyphen		71	85.008	0.83521		904
Synonymous	0.341	61	64.5	0.946	0.00000409	499
Loss of Function	2.00	7	15.5	0.452	8.31e-7	159

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000128	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000600	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.000600	0.000598
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Reversible hydration of carbon dioxide.
• Pathway: Nitrogen metabolism - Homo sapiens (human);Metabolism;Reversible hydration of carbon dioxide (Consensus)

Recessive Scores

• pRec: 0.248

Intolerance Scores

• loftool: 0.720
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.27

Haploinsufficiency Scores

• pHI: 0.224
• hipred: N
• hipred_score: 0.170
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.536

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	High	Medium	High

Mouse Genome Informatics

• Gene name: Car3
• Phenotype: muscle phenotype

Gene ontology

• Biological process: response to oxidative stress;response to bacterium;bicarbonate transport;dephosphorylation;response to ethanol
• Cellular component: cytosol
• Molecular function: carbonate dehydratase activity;zinc ion binding;nickel cation binding;phosphatase activity