MIDN

midnolin

Basic information

Region (hg38): 19:1248553-1259143

Links

ENSG00000167470 ∙ NCBI:90007 ∙ OMIM:606700 ∙ HGNC:16298 ∙ Uniprot:Q504T8 ∙ 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 MIDN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MIDN 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				2	1	3
missense			44	3		47
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region						0
non coding						0
Total	0	0	44	6	1

Variants in MIDN

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

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

Position	Type	Phenotype	Significance	ClinVar
19-1250309-C-G		not specified	Uncertain significance (Nov 14, 2023)
19-1250379-C-T		not specified	Uncertain significance (Jul 25, 2023)
19-1250389-G-C		not specified	Uncertain significance (Feb 06, 2024)
19-1250402-C-T		not specified	Uncertain significance (Mar 06, 2023)
19-1250460-G-A		not specified	Uncertain significance (Mar 14, 2023)
19-1250486-C-A		not specified	Uncertain significance (Sep 06, 2022)
19-1250493-T-G		not specified	Uncertain significance (Dec 16, 2023)
19-1250527-C-A		not specified	Uncertain significance (Dec 14, 2023)
19-1250528-A-G		not specified	Uncertain significance (Oct 03, 2023)
19-1251864-C-T		not specified	Uncertain significance (Jun 22, 2023)
19-1254163-G-GC		MIDN-related disorder	Likely benign (Mar 18, 2022)
19-1254183-C-T		not specified	Uncertain significance (Jul 09, 2021)
19-1254248-C-T		not specified	Uncertain significance (Feb 15, 2023)
19-1254278-C-G		not specified	Uncertain significance (May 02, 2024)
19-1254290-G-A		not specified	Uncertain significance (May 02, 2024)
19-1254305-G-A		MIDN-related disorder	Likely benign (Feb 18, 2022)
19-1254317-C-T		not specified	Uncertain significance (Dec 15, 2023)
19-1254344-G-C		not specified	Uncertain significance (Nov 08, 2022)
19-1254358-C-G		not specified	Uncertain significance (Mar 01, 2023)
19-1254360-G-A		not specified	Uncertain significance (Dec 26, 2023)
19-1254368-T-A		not specified	Uncertain significance (Apr 25, 2022)
19-1254405-C-T		not specified	Uncertain significance (May 23, 2023)
19-1254434-G-C		not specified	Uncertain significance (Mar 19, 2024)
19-1254437-G-A		not specified	Uncertain significance (Mar 16, 2022)
19-1254447-G-A		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MIDN	protein_coding	protein_coding	ENST00000300952	7	10591

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.179	0.819	125471	0	6	125477	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.416	280	300	0.932	0.0000214	2912
Missense in Polyphen		16	34.153	0.46848		351
Synonymous	-3.88	196	138	1.42	0.0000103	1026
Loss of Function	2.65	4	15.1	0.265	8.14e-7	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.000104	0.0000995
East Asian	0.00	0.00
Finnish	0.0000483	0.0000462
European (Non-Finnish)	0.0000277	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Facilitates ubiquitin-independent proteasomal degradation of polycomb protein CBX4. Plays a role in inhibiting the activity of glucokinase GCK and both glucose-induced and basal insulin secretion. {ECO:0000250|UniProtKB:D4AE48, ECO:0000250|UniProtKB:Q3TPJ7}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.0906
• rvis_EVS: -1.26
• rvis_percentile_EVS: 5.26

Haploinsufficiency Scores

• pHI: 0.317
• hipred: N
• hipred_score: 0.332
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.652

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Midn
• Phenotype: craniofacial phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; digestive/alimentary phenotype; reproductive system phenotype

Gene ontology

• Biological process: biological_process;negative regulation of glucokinase activity;negative regulation of insulin secretion
• Cellular component: nucleus;nucleolus;cytoplasm;cytosol
• Molecular function: molecular_function;kinase binding