CA3

protein-coding

carbonic anhydrase 3, the group of Carbonic anhydrases

Gene summary

Carbonic anhydrase III (CAIII) is a member of a multigene family (at least six separate genes are known) that encodes carbonic anhydrase isozymes. These carbonic anhydrases are a class of metalloenzymes that catalyze the reversible hydration of carbon dioxide and are differentially expressed in a number of cell types. The expression of the CA3 gene is strictly tissue specific and present at high levels in skeletal muscle and much lower levels in cardiac and smooth muscle. A proportion of carriers of Duchenne muscle dystrophy have a higher CA3 level than normal. The gene spans 10.3 kb and contains seven exons and six introns. [provided by RefSeq, Oct 2008]

MANE transcript

NM_005181.4

Inheritance

—

ClinVar variants

U:21

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr8:85,373,436-85,449,040

External References & Databases

Ensembl (ENSG00000164879)

Transcript & Mutation Effects

hg38 • Region Span ~75.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CA3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 19

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005181.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			20 clinvar			20
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	21	0	0	21

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005181.4	RefSeq	NP_005172.1	7	MANE Select
ENST00000285381.3	Ensembl	ENSP00000285381.2	7	MANE Select
ENST00000520921.1	Ensembl	ENSP00000429760.1	2	Standard
ENST00000967721.1	Ensembl	ENSP00000637780.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Nitrogen metabolism - Homo sapiens (human)
Metabolism
Reversible hydration of carbon dioxide

Biological Process

response to oxidative stress
response to bacterium
bicarbonate transport
dephosphorylation
response to ethanol

Molecular Function

carbonate dehydratase activity
zinc ion binding
nickel cation binding
phosphatase activity

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000285381
Coding exons: 7
Length: 75605
Individuals with no LoFs: 125726
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 125748
p: 0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.555	133	152	0.874	0.00000857	1705
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00060	0.00060	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Reversible hydration of carbon dioxide.;

Recessive Scores

pRec: 0.248

Intolerance Scores

LoFtool: 0.720
RVIS EVS: 0.33
RVIS percentile EVS: 73.27

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.536

Gene Damage Prediction

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