JAKMIP1

protein-coding

janus kinase and microtubule interacting protein 1

Gene summary

Enables GABA receptor binding activity and RNA binding activity. Involved in cognition. Located in membrane. Part of ribonucleoprotein complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001099433.2

Inheritance

ClinVar variants

P:1U:71B:18

Top phenotype

Intellectual disability

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr4:6,026,199-6,200,591

External References & Databases

Ensembl (ENSG00000152969)

Transcript & Mutation Effects

hg38 • Region Span ~174.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to JAKMIP1 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 61

not providedTotal: 17

Intellectual disabilityTotal: 1

Smith-Magenis Syndrome-likeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001099433.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	5 clinvar	8 clinvar	14
missense	1 clinvar		62 clinvar	5 clinvar		68
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	1	0	71	10	8	90

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001099433.2	RefSeq	NP_001092903.1	20	MANE Select
ENST00000409021.9	Ensembl	ENSP00000386711.3	20	MANE Select
NM_001306133.2	RefSeq	NP_001293062.1	12	Standard
NM_001306134.2	RefSeq	NP_001293063.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ectoderm Differentiation

Biological Process

protein transport
striatum development
cognition
positive regulation of developmental process
positive regulation of cytoplasmic translation

Molecular Function

RNA binding
mRNA binding
protein binding
microtubule binding
kinesin binding

Cellular Component

cytoplasm
microtubule
extrinsic component of membrane
ribonucleoprotein granule
ribonucleoprotein complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409021
Coding exons: 20
Length: 174393
Individuals with no LoFs: 125743
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125748
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.89	339	525	0.645	0.0000363	5394
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000026	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.291
RVIS EVS: -1.62
RVIS percentile EVS: 2.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.690

Gene Damage Prediction

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