CA9

carbonic anhydrase 9, the group of Carbonic anhydrases

Basic information

Region (hg38): 9:35673927-35681159

Links

ENSG00000107159 ∙ NCBI:768 ∙ OMIM:603179 ∙ HGNC:1383 ∙ Uniprot:Q16790 ∙ 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 CA9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CA9 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			23	5		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	5	1

Variants in CA9

This is a list of pathogenic ClinVar variants found in the CA9 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-35674143-G-A		not specified	Uncertain significance (Mar 30, 2024)
9-35674143-G-C		not specified	Uncertain significance (Jun 18, 2021)
9-35674156-C-T		not specified	Uncertain significance (Mar 30, 2024)
9-35674166-G-C		not specified	Uncertain significance (Jun 22, 2024)
9-35674167-G-T		not specified	Uncertain significance (Jan 23, 2023)
9-35674170-T-C		not specified	Likely benign (Jun 02, 2023)
9-35674203-G-T		not specified	Uncertain significance (Jan 24, 2023)
9-35674218-G-A		not specified	Uncertain significance (Mar 30, 2024)
9-35674245-C-T		not specified	Uncertain significance (Oct 03, 2022)
9-35674261-A-G		not specified	Uncertain significance (Apr 13, 2023)
9-35674273-A-C		not specified	Uncertain significance (May 28, 2024)
9-35674288-T-C		not specified	Uncertain significance (May 06, 2024)
9-35674301-T-C			Benign (Jul 06, 2018)
9-35675781-G-A		not specified	Uncertain significance (Jun 22, 2024)
9-35675854-C-T		not specified	Uncertain significance (Jan 30, 2024)
9-35675860-G-T		not specified	Uncertain significance (Dec 19, 2022)
9-35675863-C-A		not specified	Uncertain significance (Mar 29, 2024)
9-35675868-G-A		not specified	Uncertain significance (Aug 28, 2023)
9-35676076-T-C		not specified	Uncertain significance (Feb 09, 2023)
9-35676120-C-G		not specified	Uncertain significance (Dec 22, 2023)
9-35676147-G-A		not specified	Uncertain significance (Dec 06, 2022)
9-35676169-C-T		not specified	Uncertain significance (Sep 20, 2023)
9-35676324-T-C		not specified	Uncertain significance (Apr 23, 2024)
9-35676334-T-G		not specified	Uncertain significance (Sep 16, 2021)
9-35677797-C-T		not specified	Uncertain significance (Aug 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CA9	protein_coding	protein_coding	ENST00000378357	11	7304

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.30e-9	0.565	125667	0	81	125748	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.110	258	263	0.981	0.0000137	2901
Missense in Polyphen		73	79.894	0.91371		926
Synonymous	0.401	108	113	0.952	0.00000597	1008
Loss of Function	1.21	17	23.3	0.729	0.00000117	246

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000284	0.000275
Ashkenazi Jewish	0.00	0.00
East Asian	0.00152	0.00152
Finnish	0.00	0.00
European (Non-Finnish)	0.000341	0.000334
Middle Eastern	0.00152	0.00152
South Asian	0.000264	0.000261
Other	0.000336	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Reversible hydration of carbon dioxide. Participates in pH regulation. May be involved in the control of cell proliferation and transformation. Appears to be a novel specific biomarker for a cervical neoplasia. {ECO:0000269|PubMed:18703501}.
• Pathway: Nitrogen metabolism - Homo sapiens (human);Celecoxib Pathway, Pharmacodynamics;Regulation of Hypoxia-inducible Factor (HIF) by oxygen;Vitamin D Receptor Pathway;Metabolism;Reversible hydration of carbon dioxide;HIF-1-alpha transcription factor network (Consensus)

Recessive Scores

• pRec: 0.163

Intolerance Scores

• loftool: 0.903
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.47

Haploinsufficiency Scores

• pHI: 0.373
• hipred: N
• hipred_score: 0.123
• ghis: 0.384

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Car9
• Phenotype: endocrine/exocrine gland phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: morphogenesis of an epithelium;bicarbonate transport;response to testosterone;response to drug;secretion;regulation of transcription from RNA polymerase II promoter in response to hypoxia
• Cellular component: nucleolus;plasma membrane;integral component of membrane;basolateral plasma membrane;microvillus membrane
• Molecular function: carbonate dehydratase activity;protein binding;zinc ion binding