MICAL3

microtubule associated monooxygenase, calponin and LIM domain containing 3, the group of LIM domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 22:17787648-18024561

Links

ENSG00000243156 ∙ NCBI:57553 ∙ OMIM:608882 ∙ HGNC:24694 ∙ Uniprot:Q7RTP6 ∙ 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 MICAL3 gene.

• Inborn genetic diseases (100 variants)
• not provided (15 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MICAL3 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				4	2	6
missense			99	6	4	109
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	99	10	6

Variants in MICAL3

This is a list of pathogenic ClinVar variants found in the MICAL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-17790875-T-C		not specified	Uncertain significance (Jun 22, 2021)
22-17791210-C-A			Benign (Mar 02, 2018)
22-17791212-G-A			Likely benign (Sep 01, 2023)
22-17791217-G-A		not specified	Uncertain significance (Jul 06, 2021)
22-17808861-G-A		not specified	Uncertain significance (Dec 06, 2023)
22-17808877-C-T		not specified	Uncertain significance (Feb 02, 2022)
22-17808883-T-C		not specified	Uncertain significance (Nov 10, 2022)
22-17808895-G-A		not specified	Uncertain significance (Sep 25, 2023)
22-17808897-C-T		not specified	Uncertain significance (Oct 27, 2023)
22-17808900-T-C		not specified	Uncertain significance (Jan 24, 2023)
22-17810720-G-A		not specified	Uncertain significance (Jun 24, 2022)
22-17810767-C-T		not specified	Uncertain significance (Dec 01, 2022)
22-17810775-C-G			Likely benign (Sep 01, 2023)
22-17810806-G-A		not specified	Uncertain significance (Nov 18, 2022)
22-17816698-G-A			Uncertain significance (Nov 01, 2018)
22-17816729-G-A			Likely benign (Oct 01, 2022)
22-17816741-G-T		not specified	Uncertain significance (Apr 08, 2022)
22-17816769-C-T		not specified	Uncertain significance (Jan 16, 2024)
22-17816772-C-T		not specified	Uncertain significance (Dec 15, 2023)
22-17817322-A-T		not specified	Uncertain significance (Oct 12, 2022)
22-17817332-C-T		not specified	Likely benign (Jun 01, 2023)
22-17817337-T-G		not specified	Uncertain significance (Apr 13, 2022)
22-17817356-T-C		not specified	Uncertain significance (Mar 31, 2023)
22-17817359-C-T		not specified	Uncertain significance (Nov 21, 2022)
22-17817418-T-C		not specified	Uncertain significance (Jun 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MICAL3	protein_coding	protein_coding	ENST00000441493	31	236911

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.995	0.00501	125051	0	80	125131	0.000320

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.75	1028	1.20e+3	0.858	0.0000777	12907
Missense in Polyphen		385	542.31	0.70993		5776
Synonymous	-0.360	519	509	1.02	0.0000352	3993
Loss of Function	7.17	17	90.7	0.188	0.00000489	1069

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00107	0.000954
Ashkenazi Jewish	0.00	0.00
East Asian	0.000115	0.000110
Finnish	0.000378	0.000324
European (Non-Finnish)	0.000399	0.000353
Middle Eastern	0.000115	0.000110
South Asian	0.000205	0.000196
Other	0.000188	0.000164

dbNSFP

Source: dbNSFP

• Function: FUNCTION: 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. In the absence of actin, it also functions as a NADPH oxidase producing H(2)O(2). Seems to act as Rab effector protein and plays a role in vesicle trafficking. Involved in exocytic vesicles tethering and fusion: the monooxygenase activity is required for this process and implicates RAB8A associated with exocytotic vesicles. Required for cytokinesis. Contributes to stabilization and/or maturation of the intercellular bridge independently of its monooxygenase activity. Promotes recruitment of Rab8 and ERC1 to the intercellular bridge, and together these proteins are proposed to function in timely abscission. {ECO:0000269|PubMed:21596566, ECO:0000269|PubMed:24440334}.

Recessive Scores

• pRec: 0.119

Intolerance Scores

• rvis_EVS: 0.41
• rvis_percentile_EVS: 76.52

Haploinsufficiency Scores

• pHI: 0.163
• hipred: N
• hipred_score: 0.352
• ghis: 0.415

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0814

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mical3

Gene ontology

• Biological process: exocytosis;cytoskeleton organization;cell cycle;actin filament depolymerization;cell division;oxidation-reduction process
• Cellular component: nucleus;nucleoplasm;spindle;cytosol;plasma membrane;cell cortex;midbody;cell projection
• Molecular function: actin binding;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;Rab GTPase binding;metal ion binding;FAD binding