CA5B

protein-coding

carbonic anhydrase 5B, the group of Carbonic anhydrases

Gene summary

Carbonic anhydrases (CAs) are a large family of zinc metalloenzymes that catalyze the reversible hydration of carbon dioxide. They participate in a variety of biological processes, including respiration, calcification, acid-base balance, bone resorption, and the formation of aqueous humor, cerebrospinal fluid, saliva, and gastric acid. They show extensive diversity in tissue distribution and in their subcellular localization. This gene encodes carbonic anhydrase 5B. CA5B, and the related CA5A gene, has its expression localized in the mitochondria though CA5B has a wider tissue distribution than CA5A, which is restricted to the liver, kidneys, and skeletal muscle. A carbonic anhydrase pseudogene (CA5BP1) is adjacent to the CA5B gene and these two loci produce CA5BP1-CA5B readthrough transcripts. [provided by RefSeq, Jan 2019]

MANE transcript

NM_007220.4

Inheritance

—

ClinVar variants

U:88B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chrX:15,688,830-15,788,411

External References & Databases

Ensembl (ENSG00000169239)

Transcript & Mutation Effects

hg38 • Region Span ~99.6 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 CA5B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 48

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_007220.4. 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			6 clinvar			6
missense			69 clinvar	2 clinvar		71
nonsense			4 clinvar			4
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)			8 clinvar	1 clinvar		9
Total	0	0	88	3	0	91

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_007220.4	RefSeq	NP_009151.1	7	MANE Select
ENST00000318636.8	Ensembl	ENSP00000314099.3	7	MANE Select
ENST00000478341.1	Ensembl	ENSP00000417236.1	2	Standard
ENST00000479740.5	Ensembl	ENSP00000417553.1	3	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 bacterium
bicarbonate transport

Molecular Function

carbonate dehydratase activity
zinc ion binding

Cellular Component

mitochondrion
mitochondrial matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000318636
Coding exons: 7
Length: 98795
Individuals with no LoFs: 125704
Homozygous LoFs: 11
Heterozygous LoFs: 28
Defined: 125743
p: 0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0481	125	123	1.01	0.00000994	2069
Missense (PolyPhen)		53	48.558	1.0915		854
Synonymous	0.286	46	48.5	0.948	0.00000391	610
Loss of Function	1.11	7	11.0	0.637	8.12e-7	189

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000076	0.000062	rare
Latino/Admixed American	0.00048	0.00035	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000077	0.000054	rare
Finnish	0.00089	0.00065	rare
European (Non-Finnish)	0.00010	0.000070	rare
South Asian	0.00016	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Reversible hydration of carbon dioxide.;

Intolerance Scores

LoFtool: 0.639
RVIS EVS: -0.07
RVIS percentile EVS: 48.12

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.987

Gene Damage Prediction

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