JAKMIP1

janus kinase and microtubule interacting protein 1

Basic information

Region (hg38): 4:6026199-6200591

Links

ENSG00000152969 ∙ NCBI:152789 ∙ OMIM:611195 ∙ HGNC:26460 ∙ Uniprot:Q96N16 ∙ 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 JAKMIP1 gene.

• Smith-Magenis Syndrome-like (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the JAKMIP1 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	8	13
missense	1		25	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				1	2	3
non coding				1	1	2
Total	1	0	26	7	9

Variants in JAKMIP1

This is a list of pathogenic ClinVar variants found in the JAKMIP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-6029725-C-T			Likely benign (Mar 29, 2018)
4-6036057-C-T			Benign (Dec 31, 2019)
4-6036072-C-T			Benign (Dec 31, 2019)
4-6042198-G-A			Benign (Jun 10, 2018)
4-6054098-G-A			Benign (Dec 31, 2019)
4-6054100-C-G		Smith-Magenis Syndrome-like	Pathogenic (Aug 15, 2016)
4-6056726-T-C		not specified	Uncertain significance (May 09, 2022)
4-6060504-G-A		not specified	Uncertain significance (Jun 09, 2022)
4-6062330-G-A			Likely benign (Jun 25, 2018)
4-6062396-G-C			Likely benign (Apr 11, 2018)
4-6062401-G-T			Uncertain significance (Feb 12, 2021)
4-6062408-G-A			Benign (Apr 04, 2018)
4-6062442-T-C		Intellectual disability	Uncertain significance (Aug 01, 2017)
4-6064920-G-A		not specified	Uncertain significance (Jan 03, 2024)
4-6064991-T-C			Likely benign (Oct 16, 2018)
4-6065017-C-T			Likely benign (Dec 04, 2017)
4-6078946-G-A		not specified	Uncertain significance (Oct 26, 2022)
4-6078979-C-T		not specified	Uncertain significance (Dec 13, 2023)
4-6078988-C-T		not specified	Uncertain significance (May 23, 2024)
4-6080183-C-T		not specified	Uncertain significance (Jun 29, 2023)
4-6080297-C-T		not specified	Uncertain significance (Dec 02, 2021)
4-6081618-G-A			Benign (Dec 31, 2019)
4-6081672-C-G			Benign (Dec 31, 2019)
4-6081697-C-T		not specified	Uncertain significance (Jan 31, 2023)
4-6081725-G-C		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
JAKMIP1	protein_coding	protein_coding	ENST00000409021	20	174393

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000138	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.89	339	525	0.645	0.0000363	5394
Missense in Polyphen		114	216.27	0.52712		2173
Synonymous	1.20	208	231	0.900	0.0000168	1568
Loss of Function	5.89	6	51.8	0.116	0.00000280	565

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000291	0.0000291
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Associates with microtubules and may play a role in the microtubule-dependent transport of the GABA-B receptor. May play a role in JAK1 signaling and regulate microtubule cytoskeleton rearrangements. {ECO:0000269|PubMed:14718537, ECO:0000269|PubMed:15277531, ECO:0000269|PubMed:17532644}.
• Pathway: Ectoderm Differentiation (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.291
• rvis_EVS: -1.62
• rvis_percentile_EVS: 2.93

Haploinsufficiency Scores

• pHI: 0.626
• hipred: Y
• hipred_score: 0.624
• ghis: 0.594

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.690

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Jakmip1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: protein transport;striatum development;cognition;positive regulation of developmental process;positive regulation of cytoplasmic translation
• Cellular component: cytoplasm;microtubule;extrinsic component of membrane;ribonucleoprotein granule;ribonucleoprotein complex
• Molecular function: RNA binding;mRNA binding;protein binding;microtubule binding;kinesin binding;kinase binding;translation regulator activity;GABA receptor binding