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): 11:12094007-12359144

Previous symbols: [ "MICALCL" ]

Links

ENSG00000133816 ∙ NCBI:9645 ∙ OMIM:608881 ∙ HGNC:24693 ∙ Uniprot:O94851 ∙ 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 MICAL2 gene.

• Inborn genetic diseases (73 variants)
• not provided (11 variants)

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	1	3
missense			71	6	3	80
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	71	8	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)
11-12162170-G-C		not specified	Uncertain significance (Jan 04, 2022)
11-12162174-G-A		not specified	Uncertain significance (Aug 10, 2023)
11-12162238-C-G		not specified	Uncertain significance (Sep 16, 2021)
11-12162275-C-A		not specified	Uncertain significance (Dec 28, 2023)
11-12162276-C-G			Likely benign (May 30, 2018)
11-12162285-C-G		not specified	Uncertain significance (May 27, 2022)
11-12162370-G-A		not specified	Uncertain significance (Dec 01, 2022)
11-12162380-C-A		not specified	Uncertain significance (Feb 16, 2023)
11-12162415-C-A		not specified	Uncertain significance (Apr 05, 2023)
11-12204256-A-C		not specified	Uncertain significance (Dec 15, 2023)
11-12204256-A-T		not specified	Uncertain significance (Nov 08, 2022)
11-12204302-C-A		not specified	Uncertain significance (Sep 07, 2022)
11-12204325-G-A		not specified	Uncertain significance (Oct 29, 2021)
11-12204395-T-A		not specified	Uncertain significance (Dec 01, 2022)
11-12204449-A-G		not specified	Uncertain significance (Nov 10, 2022)
11-12208064-A-T		not specified	Uncertain significance (Nov 20, 2023)
11-12209524-C-T		not specified	Uncertain significance (Oct 16, 2023)
11-12209563-T-C		not specified	Uncertain significance (Nov 08, 2022)
11-12213282-A-T		not specified	Uncertain significance (Feb 13, 2024)
11-12213330-C-T		not specified	Uncertain significance (Dec 12, 2023)
11-12213377-C-G		not specified	Uncertain significance (Jun 06, 2023)
11-12216306-G-A		not specified	Uncertain significance (Jun 22, 2021)
11-12220201-G-C		not specified	Uncertain significance (Jun 09, 2022)
11-12220232-C-T		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MICAL2	protein_coding	protein_coding	ENST00000256194	25	169792

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.18e-12	1.00	123496	24	2228	125748	0.00899

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.793	612	670	0.914	0.0000409	7362
Missense in Polyphen		224	302.28	0.74104		3352
Synonymous	-1.54	300	268	1.12	0.0000168	2206
Loss of Function	3.49	29	57.6	0.503	0.00000290	670

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00471	0.00470
Ashkenazi Jewish	0.00310	0.00308
East Asian	0.000272	0.000272
Finnish	0.00694	0.00695
European (Non-Finnish)	0.0172	0.0167
Middle Eastern	0.000272	0.000272
South Asian	0.00135	0.00127
Other	0.00708	0.00703

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

• 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

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

Mouse Genome Informatics

• Gene name: Mical2

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