MIOS

meiosis regulator for oocyte development, the group of WD repeat domain containing|GATOR2 subcomplex

Basic information

Region (hg38): 7:7566875-7608932

Links

ENSG00000164654 ∙ NCBI:54468 ∙ OMIM:615359 ∙ HGNC:21905 ∙ Uniprot:Q9NXC5 ∙ 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 MIOS gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MIOS 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	1	5
missense			36			36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	4	1

Variants in MIOS

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

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

Position	Type	Phenotype	Significance	ClinVar
7-7572482-G-A		not specified	Uncertain significance (Oct 27, 2023)
7-7572617-G-A		not specified	Uncertain significance (Sep 13, 2023)
7-7572656-C-A		not specified	Uncertain significance (Dec 11, 2023)
7-7572909-G-C		not specified	Uncertain significance (Mar 20, 2023)
7-7572930-C-A		not specified	Uncertain significance (Dec 06, 2021)
7-7572947-A-T		not specified	Uncertain significance (Feb 06, 2023)
7-7572971-G-A		not specified	Uncertain significance (Oct 05, 2023)
7-7573091-C-T		not specified	Uncertain significance (Dec 20, 2023)
7-7573105-A-G		not specified	Uncertain significance (Apr 15, 2024)
7-7573139-G-A		not specified	Uncertain significance (Oct 13, 2023)
7-7573216-G-C		not specified	Uncertain significance (Mar 21, 2023)
7-7573222-A-G			Likely benign (Nov 27, 2017)
7-7573316-G-A		not specified	Uncertain significance (Aug 04, 2023)
7-7573339-G-A			Likely benign (Apr 01, 2022)
7-7573487-A-G		not specified	Uncertain significance (Mar 08, 2024)
7-7573506-A-G		not specified	Uncertain significance (Jan 31, 2024)
7-7573563-T-C		not specified	Uncertain significance (Sep 27, 2021)
7-7573590-G-A		not specified	Uncertain significance (Apr 23, 2024)
7-7573605-G-A		not specified	Uncertain significance (May 12, 2024)
7-7573644-T-C		not specified	Uncertain significance (May 31, 2022)
7-7573676-A-G		not specified	Uncertain significance (Apr 05, 2023)
7-7573688-G-C		not specified	Uncertain significance (Dec 07, 2021)
7-7573705-G-C		not specified	Uncertain significance (Jan 16, 2024)
7-7573724-G-A		not specified	Uncertain significance (May 27, 2022)
7-7573761-C-T		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MIOS	protein_coding	protein_coding	ENST00000340080	10	42058

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.89e-9	1.00	124733	0	61	124794	0.000244

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.37	386	469	0.823	0.0000240	5742
Missense in Polyphen		88	153.55	0.57311		1861
Synonymous	-1.73	192	164	1.17	0.00000864	1642
Loss of Function	3.16	22	44.9	0.490	0.00000275	515

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00104	0.00104
Ashkenazi Jewish	0.00	0.00
East Asian	0.000224	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000224	0.000223
South Asian	0.000196	0.000196
Other	0.000337	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: As a component of the GATOR subcomplex GATOR2, functions within the amino acid-sensing branch of the TORC1 signaling pathway. Indirectly activates mTORC1 and the TORC1 signaling pathway through the inhibition of the GATOR1 subcomplex (PubMed:23723238). It is negatively regulated by the upstream amino acid sensors SESN2 and CASTOR1 (PubMed:25457612, PubMed:27487210). {ECO:0000269|PubMed:23723238, ECO:0000269|PubMed:25457612, ECO:0000269|PubMed:27487210}.
• Pathway: mTOR signaling pathway - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.515
• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.21

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.426
• ghis: 0.563

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.834

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mios

Gene ontology

• Biological process: positive regulation of TOR signaling;cellular response to amino acid starvation;cellular protein-containing complex localization
• Cellular component: nucleus;nucleoplasm;lysosomal membrane;cytosol;cell junction;GATOR2 complex
• Molecular function: protein binding