CA6

carbonic anhydrase 6, the group of Carbonic anhydrases

Basic information

Region (hg38): 1:8945867-8975092

Links

ENSG00000131686 ∙ NCBI:765 ∙ OMIM:114780 ∙ HGNC:1380 ∙ Uniprot:P23280 ∙ 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 CA6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CA6 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			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	1

Variants in CA6

This is a list of pathogenic ClinVar variants found in the CA6 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-8945906-T-C		not specified	Uncertain significance (Dec 12, 2023)
1-8945924-T-C		not specified	Uncertain significance (Apr 15, 2024)
1-8945926-G-A		not specified	Uncertain significance (Nov 21, 2022)
1-8945942-A-T		not specified	Uncertain significance (Apr 23, 2024)
1-8949323-A-G		not specified	Uncertain significance (Sep 14, 2021)
1-8949334-A-G		not specified	Likely benign (Jun 29, 2022)
1-8949352-G-T		not specified	Uncertain significance (Feb 06, 2024)
1-8949359-A-G		not specified	Uncertain significance (Nov 22, 2021)
1-8949393-C-T			Benign (Jun 13, 2018)
1-8957206-T-A		not specified	Uncertain significance (Aug 03, 2022)
1-8957214-C-T		not specified	Uncertain significance (Oct 21, 2021)
1-8957259-G-A		not specified	Uncertain significance (May 03, 2023)
1-8958922-C-A		not specified	Uncertain significance (Nov 19, 2022)
1-8958982-G-A		not specified	Uncertain significance (Dec 01, 2022)
1-8967688-G-A		not specified	Likely benign (Feb 12, 2024)
1-8967769-G-A		not specified	Uncertain significance (Feb 06, 2024)
1-8967814-C-G		not specified	Uncertain significance (Jan 06, 2023)
1-8970867-G-T		not specified	Uncertain significance (Dec 07, 2023)
1-8970943-T-C		not specified	Uncertain significance (Dec 30, 2023)
1-8974627-A-G		not specified	Uncertain significance (Dec 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CA6	protein_coding	protein_coding	ENST00000377436	8	29226

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000360	0.957	125723	0	22	125745	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0794	174	177	0.983	0.00000994	2019
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000207	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000794	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Reversible hydration of carbon dioxide. Its role in saliva is unknown.
• Pathway: Nitrogen metabolism - Homo sapiens (human);Metabolism;Reversible hydration of carbon dioxide (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.759
• rvis_EVS: 0.77
• rvis_percentile_EVS: 87.06

Haploinsufficiency Scores

• pHI: 0.132
• hipred: N
• hipred_score: 0.234

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.782

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Car6
• Phenotype: immune system phenotype

Zebrafish Information Network

• Gene name: ca6
• Affected structure: swim bladder
• Phenotype tag: abnormal
• Phenotype quality: uninflated

Gene ontology

• Biological process: detection of chemical stimulus involved in sensory perception of bitter taste;one-carbon metabolic process;bicarbonate transport
• Cellular component: extracellular region;extracellular space;extracellular exosome
• Molecular function: carbonate dehydratase activity;zinc ion binding