CA12

carbonic anhydrase 12, the group of Carbonic anhydrases

Basic information

Region (hg38): 15:63321377-63381846

Links

ENSG00000074410 ∙ NCBI:771 ∙ OMIM:603263 ∙ HGNC:1371 ∙ Uniprot:O43570 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• isolated hyperchlorhidrosis (Strong), mode of inheritance: AR
• isolated hyperchlorhidrosis (Supportive), mode of inheritance: AR
• isolated hyperchlorhidrosis (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hyperchlorhidrosis, isolated	AR	Renal	In infancy, salt wasting can lead to severe hyponatremic dehydration/hyperkalemia, and precautionary measures (eg, sodium supplementation) can be beneficial	Renal	21035102; 21184099

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CA12 gene.

• Isolated hyperchlorhidrosis (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CA12 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				7	4	11
missense	1		21	4	2	28
nonsense						0
start loss						0
frameshift	1	1	1			3
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding					21	21
Total	2	1	22	11	27

Variants in CA12

This is a list of pathogenic ClinVar variants found in the CA12 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-63326051-G-A			Benign (Nov 10, 2018)
15-63326289-G-A			Likely benign (Oct 23, 2018)
15-63326293-G-A		not specified	Uncertain significance (Jul 08, 2022)
15-63326313-G-T		not specified	Uncertain significance (Aug 16, 2021)
15-63327183-CCA-C		Isolated hyperchlorhidrosis	Likely pathogenic (Mar 10, 2018)
15-63327205-G-A		CA12-related disorder	Likely benign (Jun 02, 2019)
15-63327234-C-T		Isolated hyperchlorhidrosis	Conflicting classifications of pathogenicity (Mar 22, 2023)
15-63327500-G-GT			Benign (Jun 18, 2021)
15-63328115-G-A		not specified	Uncertain significance (Apr 24, 2024)
15-63328338-CT-C			Benign (Jun 18, 2021)
15-63328338-C-CT			Benign (Jun 18, 2021)
15-63338692-C-T			Benign (Nov 10, 2018)
15-63338829-G-GAGGT		Isolated hyperchlorhidrosis	Uncertain significance (-)
15-63338833-G-GAGGT		Isolated hyperchlorhidrosis	Pathogenic (Oct 20, 2015)
15-63338888-C-G		not specified	Uncertain significance (May 04, 2022)
15-63338928-T-C			Likely benign (Jul 29, 2018)
15-63339266-T-TC			Benign (Jun 18, 2021)
15-63339269-A-AT			Benign (Nov 10, 2018)
15-63339270-CAGAG-C			Benign (Nov 10, 2018)
15-63340346-C-T		not specified	Uncertain significance (Jul 27, 2021)
15-63340367-C-G		Isolated hyperchlorhidrosis	Uncertain significance (Mar 26, 2024)
15-63340370-C-T		CA12-related disorder	Benign (Feb 22, 2019)
15-63340371-G-A		not specified	Uncertain significance (Oct 12, 2021)
15-63340389-C-G		not specified	Uncertain significance (Dec 28, 2022)
15-63340443-G-C		not specified	Uncertain significance (Nov 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CA12	protein_coding	protein_coding	ENST00000178638	11	60784

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.28e-11	0.0966	125477	0	271	125748	0.00108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.184	203	196	1.04	0.0000118	2296
Missense in Polyphen		75	75.806	0.98937		871
Synonymous	-0.920	99	88.0	1.12	0.00000635	697
Loss of Function	0.437	18	20.1	0.895	9.65e-7	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00263	0.00263
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000326	0.000326
Finnish	0.000326	0.000323
European (Non-Finnish)	0.00142	0.00142
Middle Eastern	0.000326	0.000326
South Asian	0.000164	0.000163
Other	0.000979	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Reversible hydration of carbon dioxide.
• Pathway: Nitrogen metabolism - Homo sapiens (human);Celecoxib Pathway, Pharmacodynamics;miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Metabolism;Reversible hydration of carbon dioxide (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.901
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.31

Haploinsufficiency Scores

• pHI: 0.213
• hipred: N
• hipred_score: 0.197
• ghis: 0.598

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.996

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Car12
• 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)

Gene ontology

• Biological process: bicarbonate transport;chloride ion homeostasis
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: carbonate dehydratase activity;zinc ion binding