MICAL2

microtubule associated monooxygenase, calponin and LIM domain containing 2, the group of MicroRNA protein coding host genes|LIM domain containing

Basic information

Region (hg38): 11:12094008-12359144

Previous symbols: [ "MICALCL" ]

Links

ENSG00000133816NCBI:9645OMIM:608881HGNC:24693Uniprot:O94851AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MICAL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MICAL2 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
2
clinvar
1
clinvar
3
missense
125
clinvar
11
clinvar
3
clinvar
139
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
0
Total 0 0 125 13 4

Variants in MICAL2

This is a list of pathogenic ClinVar variants found in the MICAL2 region.

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

Position Type Phenotype Significance ClinVar
11-12162163-A-T not specified Uncertain significance (Jul 08, 2022)2209423
11-12162170-G-C not specified Uncertain significance (Jan 04, 2022)2269920
11-12162174-G-A not specified Uncertain significance (Aug 10, 2023)2617873
11-12162186-C-A not specified Uncertain significance (May 02, 2024)3294747
11-12162238-C-G not specified Uncertain significance (Sep 16, 2021)2251102
11-12162275-C-A not specified Uncertain significance (Dec 28, 2023)3126137
11-12162276-C-G Likely benign (May 30, 2018)786189
11-12162285-C-G not specified Uncertain significance (May 27, 2022)2378065
11-12162370-G-A not specified Uncertain significance (Dec 01, 2022)2368247
11-12162380-C-A not specified Uncertain significance (Feb 16, 2023)2486334
11-12162415-C-A not specified Uncertain significance (Apr 05, 2023)2524892
11-12204256-A-C not specified Uncertain significance (Dec 15, 2023)3126169
11-12204256-A-T not specified Uncertain significance (Nov 08, 2022)2324666
11-12204302-C-A not specified Uncertain significance (Sep 07, 2022)2311192
11-12204325-G-A not specified Uncertain significance (Oct 29, 2021)2257957
11-12204395-T-A not specified Uncertain significance (Dec 01, 2022)2331179
11-12204449-A-G not specified Uncertain significance (Nov 10, 2022)2218309
11-12208064-A-T not specified Uncertain significance (Nov 20, 2023)3126184
11-12209508-C-T not specified Uncertain significance (May 30, 2024)3294750
11-12209524-C-T not specified Uncertain significance (Oct 16, 2023)3126185
11-12209563-T-C not specified Uncertain significance (Nov 08, 2022)2324814
11-12213282-A-T not specified Uncertain significance (Feb 13, 2024)3126187
11-12213330-C-T not specified Uncertain significance (Dec 12, 2023)3126189
11-12213377-C-G not specified Uncertain significance (Jun 06, 2023)2545362
11-12216236-A-G not specified Uncertain significance (Apr 01, 2024)3294732

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
MICAL2protein_codingprotein_codingENST00000256194 25169792
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.18e-121.001234962422281257480.00899
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7936126700.9140.00004097362
Missense in Polyphen224302.280.741043352
Synonymous-1.543002681.120.00001682206
Loss of Function3.492957.60.5030.00000290670

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.004710.00470
Ashkenazi Jewish0.003100.00308
East Asian0.0002720.000272
Finnish0.006940.00695
European (Non-Finnish)0.01720.0167
Middle Eastern0.0002720.000272
South Asian0.001350.00127
Other0.007080.00703

dbNSFP

Source: dbNSFP

Function
FUNCTION: Nuclear monooxygenase that promotes depolymerization of F-actin by mediating oxidation of specific methionine residues on actin to form methionine-sulfoxide, resulting in actin filament disassembly and preventing repolymerization (PubMed:24440334). In the absence of actin, it also functions as a NADPH oxidase producing H(2)O(2) (By similarity). Acts as a key regulator of the SRF signaling pathway elicited by nerve growth factor and serum: mediates oxidation and subsequent depolymerization of nuclear actin, leading to increase MKL1/MRTF-A presence in the nucleus and promote SRF:MKL1/MRTF-A-dependent gene transcription. Does not activate SRF:MKL1/MRTF-A through RhoA (PubMed:24440334). {ECO:0000250|UniProtKB:Q8TDZ2, ECO:0000269|PubMed:24440334}.;

Recessive Scores

pRec
0.103

Intolerance Scores

loftool
rvis_EVS
0.55
rvis_percentile_EVS
81.23

Haploinsufficiency Scores

pHI
0.357
hipred
N
hipred_score
0.463
ghis
0.518

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.151

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Mical2
Phenotype

Gene ontology

Biological process
heart looping;cytoskeleton organization;heart development;positive regulation of transcription via serum response element binding;sulfur oxidation;actin filament depolymerization;oxidation-reduction process
Cellular component
nucleus
Molecular function
actin binding;NAD(P)H oxidase activity;oxidoreductase activity;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen;NADPH:sulfur oxidoreductase activity;metal ion binding;FAD binding