JAKMIP3

protein-coding

Janus kinase and microtubule interacting protein 3

Gene summary

Predicted to enable kinase binding activity and microtubule binding activity. Predicted to be located in Golgi apparatus. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C10orf39
C10orf14

MANE transcript

NM_001323087.2

Inheritance

—

ClinVar variants

U:140B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr10:132,036,336-132,184,858

External References & Databases

Ensembl (ENSG00000188385)

Transcript & Mutation Effects

hg38 • Region Span ~148.5 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to JAKMIP3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 141

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001323087.2. 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	2 clinvar		3
missense			139 clinvar	2 clinvar		141
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	140	4	0	144

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 79 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001323087.2	RefSeq	NP_001310016.1	21	MANE Select
ENST00000684848.1	Ensembl	ENSP00000508932.1	21	MANE Select
NM_001105521.4	RefSeq	NP_001098991.1	21	Standard
NM_001323086.2	RefSeq	NP_001310015.1	22	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

microtubule binding
kinase binding

Cellular Component

Golgi apparatus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000298622
Coding exons: 21
Length: 80139
Individuals with no LoFs: 125522
Homozygous LoFs: 0
Heterozygous LoFs: 122
Defined: 125644
p: 0.000486

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.32	425	509	0.835	0.0000341	5458
Missense (PolyPhen)		133	189.09	0.70337		2027
Synonymous	-1.19	243	221	1.10	0.0000162	1556
Loss of Function	5.00	13	51.8	0.251	0.00000262	602

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00071	0.00062	rare
Latino/Admixed American	0.00042	0.00040	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.0011	0.0011	notable
European (Non-Finnish)	0.00073	0.00061	rare
South Asian	0.00011	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.691
RVIS EVS: -1.74
RVIS percentile EVS: 2.42

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.197

Gene Damage Prediction

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