MICALL2

MICAL like 2, the group of LIM domain containing

Basic information

Region (hg38): 7:1428465-1459470

Links

ENSG00000164877 ∙ NCBI:79778 ∙ ∙ HGNC:29672 ∙ Uniprot:Q8IY33 ∙ 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 MICALL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MICALL2 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				8	11	19
missense			98	12	13	123
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	98	20	25

Variants in MICALL2

This is a list of pathogenic ClinVar variants found in the MICALL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-1434624-G-A			Benign (Apr 30, 2018)
7-1434636-T-C		not specified	Uncertain significance (Nov 20, 2023)
7-1434644-G-C			Likely benign (Apr 06, 2018)
7-1434646-G-A		not specified	Uncertain significance (Dec 14, 2021)
7-1434651-T-G			Benign (Dec 31, 2019)
7-1435122-G-A		not specified	Uncertain significance (Apr 26, 2023)
7-1435129-C-G		not specified	Uncertain significance (Dec 05, 2022)
7-1435155-G-A			Benign (Dec 31, 2019)
7-1436758-C-T		not specified	Uncertain significance (Sep 17, 2021)
7-1436761-G-A			Benign/Likely benign (May 01, 2023)
7-1436770-C-A		not specified	Uncertain significance (May 10, 2023)
7-1436785-C-T		not specified	Uncertain significance (Jun 27, 2022)
7-1436786-G-A			Likely benign (May 14, 2018)
7-1436791-C-T		not specified	Uncertain significance (Dec 28, 2023)
7-1436822-C-G		not specified	Uncertain significance (Apr 07, 2023)
7-1437547-T-C		not specified	Uncertain significance (Feb 06, 2023)
7-1437553-G-A		not specified	Conflicting classifications of pathogenicity (Apr 12, 2022)
7-1437556-G-A		not specified	Uncertain significance (Oct 29, 2021)
7-1437576-A-C		not specified	Uncertain significance (Mar 05, 2024)
7-1437577-G-C		not specified	Uncertain significance (Mar 05, 2024)
7-1437594-C-T		not specified	Uncertain significance (Sep 22, 2022)
7-1437897-T-C		not specified	Uncertain significance (Nov 10, 2022)
7-1437924-G-A		not specified	Uncertain significance (Aug 16, 2021)
7-1437960-T-C		not specified	Uncertain significance (Nov 08, 2022)
7-1437975-C-T		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MICALL2	protein_coding	protein_coding	ENST00000297508	17	31038

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.44e-26	0.000129	125360	1	104	125465	0.000419

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.99	675	544	1.24	0.0000356	5650
Missense in Polyphen		180	160.87	1.1189		1719
Synonymous	-4.07	323	242	1.33	0.0000174	1883
Loss of Function	-0.264	38	36.3	1.05	0.00000178	428

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000920	0.000872
Ashkenazi Jewish	0.000407	0.000398
East Asian	0.000452	0.000435
Finnish	0.000189	0.000185
European (Non-Finnish)	0.000364	0.000353
Middle Eastern	0.000452	0.000435
South Asian	0.000892	0.000850
Other	0.000346	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Effector of small Rab GTPases which is involved in junctional complexes assembly through the regulation of cell adhesion molecules transport to the plasma membrane and actin cytoskeleton reorganization. Regulates the endocytic recycling of occludins, claudins and E-cadherin to the plasma membrane and may thereby regulate the establishment of tight junctions and adherens junctions. In parallel, may regulate actin cytoskeleton reorganization directly through interaction with F-actin or indirectly through actinins and filamins. Most probably involved in the processes of epithelial cell differentiation, cell spreading and neurite outgrowth (By similarity). {ECO:0000250}.
• Pathway: Tight junction - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0834

Intolerance Scores

• loftool: 0.725
• rvis_EVS: 1.39
• rvis_percentile_EVS: 94.66

Haploinsufficiency Scores

• pHI: 0.274
• hipred: N
• hipred_score: 0.146
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.120

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Micall2

Zebrafish Information Network

• Gene name: micall2b
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: increased speed

Gene ontology

• Biological process: actin filament polymerization;neuron projection development;actin cytoskeleton reorganization;endocytic recycling;substrate adhesion-dependent cell spreading;bicellular tight junction assembly;positive regulation of protein targeting to mitochondrion
• Cellular component: stress fiber;cytosol;plasma membrane;cell-cell junction;bicellular tight junction;actin filament bundle;neuron projection;recycling endosome
• Molecular function: protein binding;Rab GTPase binding;filamin binding;actinin binding;metal ion binding;actin filament binding