CA6

protein-coding

carbonic anhydrase 6, the group of Carbonic anhydrases

Gene summary

The protein encoded by this gene is one of several isozymes of carbonic anhydrase. This protein is found only in salivary glands and saliva and protein may play a role in the reversible hydratation of carbon dioxide though its function in saliva is unknown. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001215.4

Inheritance

—

ClinVar variants

U:48B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr1:8,945,867-8,975,092

External References & Databases

Ensembl (ENSG00000131686)

Transcript & Mutation Effects

hg38 • Region Span ~29.2 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 CA6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 51

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001215.4. 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					2 clinvar	2
missense			48 clinvar	4 clinvar		52
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	48	4	2	54

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001215.4	RefSeq	NP_001206.2	8	MANE Select
ENST00000377443.7	Ensembl	ENSP00000366662.2	8	MANE Select
NM_001270500.2	RefSeq	NP_001257429.1	8	Standard
NM_001270501.2	RefSeq	NP_001257430.1	7	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ca6	Danio rerio	Structure: swim bladder Quality: uninflated abnormal

Gene / Model

Organism

Observed Phenotype

ca6

Danio rerio

Structure: swim bladder

Quality: uninflated

abnormal

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

detection of chemical stimulus involved in sensory perception of bitter taste
one-carbon metabolic process
bicarbonate transport

Molecular Function

carbonate dehydratase activity
zinc ion binding

Cellular Component

extracellular region
extracellular space
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000377436
Coding exons: 8
Length: 29226
Individuals with no LoFs: 125723
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 125745
p: 0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0794	174	177	0.983	0.00000994	2019
Missense (PolyPhen)		69	65.763	1.0492		781
Synonymous	0.799	67	75.9	0.883	0.00000488	598
Loss of Function	1.81	8	15.7	0.508	6.70e-7	177

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000079	0.000079	rare
South Asian	0.00020	0.00020	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Reversible hydration of carbon dioxide. Its role in saliva is unknown.;

Recessive Scores

pRec: 0.114

Intolerance Scores

LoFtool: 0.759
RVIS EVS: 0.77
RVIS percentile EVS: 87.06

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.782

Gene Damage Prediction

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