MICALL1

MICAL like 1, the group of LIM domain containing

Basic information

Region (hg38): 22:37905657-37942822

Links

ENSG00000100139 ∙ NCBI:85377 ∙ OMIM:619563 ∙ HGNC:29804 ∙ Uniprot:Q8N3F8 ∙ 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 MICALL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MICALL1 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						0
missense			97	4		101
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	97	4	0

Variants in MICALL1

This is a list of pathogenic ClinVar variants found in the MICALL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-37906508-G-A		not specified	Uncertain significance (Jan 17, 2023)
22-37906556-G-A		not specified	Uncertain significance (Dec 05, 2022)
22-37906565-T-G		not specified	Uncertain significance (Feb 12, 2025)
22-37911978-A-G		not specified	Uncertain significance (Nov 08, 2024)
22-37911995-C-T		not specified	Uncertain significance (Nov 12, 2024)
22-37911996-G-A		not specified	Uncertain significance (Mar 16, 2024)
22-37912421-G-C		not specified	Uncertain significance (Jan 23, 2025)
22-37912423-G-A		not specified	Uncertain significance (Nov 21, 2022)
22-37912429-G-C		not specified	Uncertain significance (Feb 03, 2022)
22-37917736-G-A		not specified	Uncertain significance (Sep 14, 2021)
22-37917740-C-T		not specified	Uncertain significance (Sep 23, 2023)
22-37919039-G-A		not specified	Uncertain significance (Jan 18, 2025)
22-37919048-T-G		not specified	Uncertain significance (Nov 24, 2024)
22-37919172-G-C		not specified	Uncertain significance (Mar 25, 2024)
22-37921991-A-T		not specified	Uncertain significance (Jan 04, 2024)
22-37922010-A-C		not specified	Uncertain significance (May 02, 2024)
22-37922070-C-T		not specified	Uncertain significance (Aug 30, 2021)
22-37922078-C-G		not specified	Uncertain significance (Apr 06, 2022)
22-37922082-C-T		not specified	Uncertain significance (Dec 19, 2022)
22-37922105-T-C		not specified	Likely benign (Aug 22, 2023)
22-37922138-G-A		not specified	Uncertain significance (Mar 06, 2023)
22-37922157-T-G		not specified	Uncertain significance (Feb 07, 2025)
22-37922166-G-A		not specified	Uncertain significance (May 26, 2022)
22-37922214-A-G		not specified	Uncertain significance (Nov 13, 2024)
22-37922232-G-A		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MICALL1	protein_coding	protein_coding	ENST00000215957	16	37166

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.20e-7	0.997	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.976	444	506	0.878	0.0000311	5530
Missense in Polyphen		132	183.87	0.7179		2041
Synonymous	0.942	196	214	0.918	0.0000138	1790
Loss of Function	2.69	17	33.9	0.501	0.00000152	431

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000437	0.000425
Ashkenazi Jewish	0.00	0.00
East Asian	0.000383	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000230	0.000202
Middle Eastern	0.000383	0.000381
South Asian	0.0000980	0.0000980
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable lipid-binding protein with higher affinity for phosphatidic acid, a lipid enriched in recycling endosome membranes. On endosome membranes, may act as a downstream effector of Rab proteins recruiting cytosolic proteins to regulate membrane tubulation. May be involved in a late step of receptor-mediated endocytosis regulating for instance endocytosed-EGF receptor trafficking. Alternatively, may regulate slow endocytic recycling of endocytosed proteins back to the plasma membrane. May indirectly play a role in neurite outgrowth. {ECO:0000269|PubMed:19864458, ECO:0000269|PubMed:20801876, ECO:0000269|PubMed:21795389, ECO:0000269|PubMed:23596323}.

Recessive Scores

• pRec: 0.0874

Intolerance Scores

• loftool: 0.535
• rvis_EVS: -0.79
• rvis_percentile_EVS: 12.57

Haploinsufficiency Scores

• pHI: 0.0794
• hipred: N
• hipred_score: 0.448
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.625

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Micall1

Gene ontology

• Biological process: protein targeting to membrane;endocytosis;receptor-mediated endocytosis;neuron projection development;slow endocytic recycling;protein localization to endosome;plasma membrane tubulation;cellular response to nerve growth factor stimulus;retrograde transport, endosome to plasma membrane
• Cellular component: early endosome;late endosome;trans-Golgi network;extrinsic component of membrane;late endosome membrane;recycling endosome membrane
• Molecular function: protein binding;Rab GTPase binding;identical protein binding;cadherin binding;metal ion binding;phosphatidic acid binding