MINK1

misshapen like kinase 1, the group of Armadillo like helical domain containing|STRIPAK complex

Basic information

Region (hg38): 17:4833339-4898061

Links

ENSG00000141503 ∙ NCBI:50488 ∙ OMIM:609426 ∙ HGNC:17565 ∙ Uniprot:Q8N4C8 ∙ 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 MINK1 gene.

• Inborn genetic diseases (42 variants)
• Congenital myasthenic syndrome (17 variants)
• not provided (10 variants)
• Congenital Myasthenic Syndrome, Dominant/Recessive (3 variants)
• Autism;Attention deficit hyperactivity disorder;Epicanthus;Seizure;Delayed speech and language development (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MINK1 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				5	2	7
missense			43	2	1	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			12	1	7	20
Total	0	0	55	8	10

Variants in MINK1

This is a list of pathogenic ClinVar variants found in the MINK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-4833589-C-T			Likely benign (Apr 01, 2023)
17-4833603-C-T		not specified	Uncertain significance (Sep 21, 2023)
17-4881229-G-C		not specified	Uncertain significance (Apr 20, 2023)
17-4885487-T-G		not specified	Uncertain significance (Nov 03, 2022)
17-4886122-C-A		not specified	Uncertain significance (Dec 19, 2022)
17-4886545-C-T		not specified	Uncertain significance (Oct 17, 2023)
17-4887133-G-A		not specified	Uncertain significance (Feb 10, 2023)
17-4887675-A-G		not specified	Uncertain significance (Nov 16, 2021)
17-4887690-A-T		not specified	Uncertain significance (Sep 16, 2021)
17-4887708-C-G		not specified	Uncertain significance (Jun 01, 2023)
17-4887776-C-T		not specified	Uncertain significance (Apr 04, 2023)
17-4890656-T-C		not specified	Uncertain significance (Jan 03, 2024)
17-4890665-G-C		not specified	Uncertain significance (Jun 18, 2021)
17-4890959-G-C		not specified	Uncertain significance (Feb 23, 2023)
17-4891112-G-C		not specified	Uncertain significance (Feb 10, 2023)
17-4891588-G-A		not specified	Likely benign (Dec 08, 2023)
17-4891609-G-A		not specified	Uncertain significance (Jan 29, 2024)
17-4891665-C-G			Likely benign (Sep 01, 2022)
17-4891675-C-A		not specified	Uncertain significance (May 23, 2023)
17-4891678-C-A		not specified	Uncertain significance (Jun 03, 2022)
17-4891690-C-T		not specified	Uncertain significance (Mar 27, 2023)
17-4891702-G-A		not specified	Uncertain significance (May 22, 2023)
17-4892153-C-G		not specified	Uncertain significance (Jun 09, 2022)
17-4892172-C-T			Likely benign (Jul 01, 2022)
17-4892189-C-T		not specified	Uncertain significance (Oct 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MINK1	protein_coding	protein_coding	ENST00000355280	32	64674

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	7.52e-10	124733	0	10	124743	0.0000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.08	483	810	0.596	0.0000525	8545
Missense in Polyphen		132	281.39	0.4691		2883
Synonymous	-1.25	354	325	1.09	0.0000214	2590
Loss of Function	7.76	5	79.8	0.0627	0.00000474	815

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000646	0.0000644
Ashkenazi Jewish	0.00	0.00
East Asian	0.000113	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000540	0.0000530
Middle Eastern	0.000113	0.000111
South Asian	0.0000347	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine kinase which acts as a negative regulator of Ras-related Rap2-mediated signal transduction to control neuronal structure and AMPA receptor trafficking. Required for normal synaptic density, dendrite complexity, as well as surface AMPA receptor expression in hippocampal neurons. Can activate the JNK and MAPK14/p38 pathways and mediates stimulation of the stress-activated protein kinase MAPK14/p38 MAPK downstream of the Raf/ERK pathway. Phosphorylates: TANC1 upon stimulation by RAP2A, MBP and SMAD1. Has an essential function in negative selection of thymocytes, perhaps by coupling NCK1 to activation of JNK1.
• Pathway: EGF-Core;Oxidative Stress Induced Senescence;Angiopoietin Like Protein 8 Regulatory Pathway;Insulin Signaling;Oxidative Stress Induced Senescence;Cellular Senescence;Cellular responses to stress;Cellular responses to external stimuli;EGFR1 (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.404
• rvis_EVS: -1.46
• rvis_percentile_EVS: 3.86

Haploinsufficiency Scores

• pHI: 0.470
• hipred: Y
• hipred_score: 0.613
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.986

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mink1

Gene ontology

• Biological process: MAPK cascade;regulation of cell-matrix adhesion;protein phosphorylation;JNK cascade;chemical synaptic transmission;multicellular organism development;regulation of cell-cell adhesion;signal transduction by protein phosphorylation;microvillus assembly;regulation of cell migration;stress-activated protein kinase signaling cascade;actin cytoskeleton reorganization;activation of protein kinase activity;positive regulation of JNK cascade;protein autophosphorylation;neuron projection morphogenesis;dendrite morphogenesis;positive regulation of p38MAPK cascade;regulation of AMPA receptor activity
• Cellular component: cytoplasm;Golgi apparatus;cytosol;postsynaptic density;cell junction;axon;dendrite;postsynaptic membrane;extracellular exosome
• Molecular function: protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding