CA10

protein-coding

carbonic anhydrase 10, the group of Carbonic anhydrases

Gene summary

This gene encodes a protein that belongs to the carbonic anhydrase family of zinc metalloenzymes, which catalyze the reversible hydration of carbon dioxide in various biological processes. The protein encoded by this gene is an acatalytic member of the alpha-carbonic anhydrase subgroup, and it is thought to play a role in the central nervous system, especially in brain development. Multiple transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_020178.5

Inheritance

—

ClinVar variants

U:39

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr17:51,630,313-52,160,017

External References & Databases

Ensembl (ENSG00000154975)

Transcript & Mutation Effects

hg38 • Region Span ~529.7 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 CA10 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 36

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020178.5. 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						0
missense			37 clinvar			37
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	39	0	0	39

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020178.5	RefSeq	NP_064563.1	9	MANE Select
ENST00000451037.7	Ensembl	ENSP00000405388.2	9	MANE Select
NM_001082533.1	RefSeq	NP_001076002.1	9	Standard
NM_001082534.2	RefSeq	NP_001076003.1	9	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ca10b	Danio rerio	Structure: post-vent region Quality: apoptotic abnormal

Gene / Model

Organism

Observed Phenotype

ca10b

Danio rerio

Structure: post-vent region

Quality: apoptotic

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

brain development

Molecular Function

molecular_function
carbonate dehydratase activity
zinc ion binding

Cellular Component

cellular_component

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000451037
Coding exons: 9
Length: 529704
Individuals with no LoFs: 125720
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125726
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.11	144	187	0.771	0.00000987	2170
Missense (PolyPhen)		45	71.422	0.63006		790
Synonymous	0.121	65	66.3	0.981	0.00000346	598
Loss of Function	3.30	4	19.9	0.201	0.00000109	207

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Does not have a catalytic activity.;

Recessive Scores

pRec: 0.0976

Intolerance Scores

LoFtool: 0.454
RVIS EVS: -0.58
RVIS percentile EVS: 18.44

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.167

Gene Damage Prediction

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