MICAL2
Basic information
Region (hg38): 11:12094008-12359144
Previous symbols: [ "MICALCL" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 3 | |||||
missense | 125 | 11 | 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) | ||
11-12162170-G-C | not specified | Uncertain significance (Jan 04, 2022) | ||
11-12162174-G-A | not specified | Uncertain significance (Aug 10, 2023) | ||
11-12162186-C-A | not specified | Uncertain significance (May 02, 2024) | ||
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) | ||
11-12209508-C-T | not specified | Uncertain significance (May 30, 2024) | ||
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) | ||
11-12216236-A-G | not specified | Uncertain significance (Apr 01, 2024) |
GnomAD
Source:
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:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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