JAKMIP3

Summary

JAKMIP3 (Janus kinase and microtubule interacting protein 3, HGNC:23523) is a protein-coding gene on chromosome 10q26.3, encoding Janus kinase and microtubule-interacting protein 3 (Q5VZ66).

Predicted to enable kinase binding activity and microtubule binding activity. Predicted to be located in Golgi apparatus and membrane.

Source: NCBI Gene 282973 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 154 total
• MANE Select transcript: NM_001323087

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23523
Approved symbol	JAKMIP3
Name	Janus kinase and microtubule interacting protein 3
Location	10q26.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ37857, NECC2, KIAA4091, bA140A10.5
Ensembl gene	ENSG00000188385
Ensembl biotype	protein_coding
OMIM	611198
Entrez	282973

Gene structure

Transcript identifiers

Ensembl transcripts: 26 — 20 protein_coding, 5 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000298622, ENST00000477275, ENST00000653512, ENST00000653623, ENST00000654224, ENST00000657318, ENST00000657785, ENST00000657994, ENST00000658847, ENST00000659050, ENST00000659220, ENST00000660144, ENST00000661339, ENST00000662086, ENST00000664697, ENST00000665805, ENST00000666210, ENST00000666974, ENST00000667210, ENST00000668452, ENST00000669241, ENST00000669493, ENST00000669891, ENST00000670120, ENST00000670443, ENST00000684848

RefSeq mRNA: 35 — MANE Select: NM_001323087 NM_001105521, NM_001323086, NM_001323087, NM_001323088, NM_001323089, NM_001323090, NM_001392039, NM_001392040, NM_001392041, NM_001392042, NM_001392043, NM_001392044, NM_001392045, NM_001392046, NM_001392047, NM_001392048, NM_001392049, NM_001392050, NM_001392051, NM_001392052, NM_001392053, NM_001392054, NM_001392055, NM_001392056, NM_001392057, NM_001392058, NM_001392059, NM_001392060, NM_001392061, NM_001392062, NM_001392063, NM_001392064, NM_001392065, NM_001392066, NM_001392067

CCDS: CCDS44494, CCDS91378, CCDS91379, CCDS91380, CCDS91381, CCDS91382, CCDS91383, CCDS91384, CCDS91385, CCDS91386

Canonical transcript exons

ENST00000684848 — 24 exons

Exon	Start	End
ENSE00001378454	132167953	132169033
ENSE00001447619	132166983	132167055
ENSE00001600714	132141920	132142048
ENSE00001603031	132135041	132135160
ENSE00001688152	132135930	132136076
ENSE00001703981	132138119	132138178
ENSE00001722320	132137254	132137289
ENSE00001728840	132117077	132117574
ENSE00001736561	132133312	132133527
ENSE00001780209	132140451	132140579
ENSE00001804364	132137019	132137150
ENSE00003506621	132147952	132148050
ENSE00003516919	132153759	132153827
ENSE00003519491	132145518	132145580
ENSE00003531540	132163209	132163412
ENSE00003542795	132164670	132164735
ENSE00003578297	132153913	132153990
ENSE00003588532	132149412	132149510
ENSE00003605390	132145107	132145190
ENSE00003607825	132152958	132153023
ENSE00003860692	132065946	132066061
ENSE00003863327	132149982	132150041
ENSE00003868677	132104672	132104943
ENSE00003880538	132182357	132184858

Expression profiles

Bgee: expression breadth ubiquitous, 179 present calls, max score 88.36.

FANTOM5 (CAGE): breadth broad, TPM avg 2.0310 / max 271.3708, expressed in 264 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
107698	0.8453	148
107699	0.5116	120
107692	0.2714	110
107694	0.1455	54
107693	0.1004	67
107697	0.0994	57
107695	0.0356	18
107696	0.0217	15

Top tissues by expression

255 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
C1 segment of cervical spinal cord	UBERON:0006469	88.36	gold quality
spinal cord	UBERON:0002240	87.10	gold quality
corpus callosum	UBERON:0002336	86.31	gold quality
right hemisphere of cerebellum	UBERON:0014890	85.28	gold quality
right frontal lobe	UBERON:0002810	85.01	gold quality
postcentral gyrus	UBERON:0002581	84.99	gold quality
pituitary gland	UBERON:0000007	84.59	gold quality
cerebellar hemisphere	UBERON:0002245	84.46	gold quality
cerebellar cortex	UBERON:0002129	84.37	gold quality
cerebellum	UBERON:0002037	83.78	gold quality
Brodmann (1909) area 9	UBERON:0013540	83.78	gold quality
adenohypophysis	UBERON:0002196	83.77	gold quality
hypothalamus	UBERON:0001898	83.52	gold quality
substantia nigra	UBERON:0002038	83.48	gold quality
middle temporal gyrus	UBERON:0002771	83.45	gold quality
Ammon’s horn	UBERON:0001954	83.42	gold quality
parietal lobe	UBERON:0001872	82.80	gold quality
midbrain	UBERON:0001891	82.48	gold quality
primary visual cortex	UBERON:0002436	82.28	gold quality
superior frontal gyrus	UBERON:0002661	82.12	gold quality
anterior cingulate cortex	UBERON:0009835	81.78	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	81.48	gold quality
frontal cortex	UBERON:0001870	81.26	gold quality
brain	UBERON:0000955	81.05	gold quality
Brodmann (1909) area 23	UBERON:0013554	80.96	gold quality
neocortex	UBERON:0001950	80.95	gold quality
cerebral cortex	UBERON:0000956	80.89	gold quality
amygdala	UBERON:0001876	80.86	gold quality
forebrain	UBERON:0001890	80.77	gold quality
occipital lobe	UBERON:0002021	80.38	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	3.40

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	jakmip3	ENSDARG00000100708
mus_musculus	Jakmip3	ENSMUSG00000056856
rattus_norvegicus	Jakmip3	ENSRNOG00000027590

Paralogs (2): JAKMIP1 (ENSG00000152969), JAKMIP2 (ENSG00000176049)

Protein

Protein identifiers

Janus kinase and microtubule-interacting protein 3 — Q5VZ66 (reviewed: Q5VZ66)

Alternative names: Neuroendocrine long coiled-coil protein 2

All UniProt accessions (14): A0A590UIU4, A0A590UJ09, A0A590UJ61, A0A590UJC8, A0A590UJF4, A0A590UJG1, A0A590UJH1, A0A590UJQ3, A0A590UJS0, A0A590UJT1, A0A590UK11, A0A590UK42, A0A590UK98, Q5VZ66

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Golgi apparatus.

Tissue specificity. Specifically expressed in the CNS and endocrine tissues. Also detected in other tissues including heart, testis and prostate.

Similarity. Belongs to the JAKMIP family.

RefSeq proteins (35): NP_001098991, NP_001310015, NP_001310016, NP_001310017, NP_001310018, NP_001310019, NP_001378968, NP_001378969, NP_001378970, NP_001378971, NP_001378972, NP_001378973, NP_001378974, NP_001378975, NP_001378976, NP_001378977, NP_001378978, NP_001378979, NP_001378980, NP_001378981, NP_001378982, NP_001378983, NP_001378984, NP_001378985, NP_001378986, NP_001378987, NP_001378988, NP_001378989, NP_001378990, NP_001378991, NP_001378992, NP_001378993, NP_001378994, NP_001378995, NP_001378996 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR024836	JAKMIP	Family
IPR031994	JAKMIP_C	Domain

Pfam: PF16034

UniProt features (13 total): coiled-coil region 4, compositionally biased region 3, region of interest 2, sequence variant 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5VZ66-F1	79.62	0.35

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 384

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 65 (showing top): LFA1_Q6, CAGCTG_AP4_Q5, GTGCCTT_MIR506, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, VDR_Q3, TGCCTTA_MIR124A, GOMF_CYTOSKELETAL_PROTEIN_BINDING, GOMF_KINASE_BINDING, GSE13762_CTRL_VS_125_VITAMIND_DAY5_DC_UP, CAGTATT_MIR200B_MIR200C_MIR429, NFE2L2.V2, MIR8485, MIR548AR_3P, MIR506_3P, MIR124_3P

GO Biological Process (0):

GO Molecular Function (2): microtubule binding (GO:0008017), kinase binding (GO:0019900)

GO Cellular Component (2): Golgi apparatus (GO:0005794), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
tubulin binding	1
enzyme binding	1
cytoplasm	1
endomembrane system	1
intracellular membrane-bounded organelle	1
cellular anatomical structure	1

Protein interactions and networks

STRING

438 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
JAKMIP3	C2orf81	A6NN90	530
JAKMIP3	CCDC154	A6NI56	507
JAKMIP3	SMCO3	A2RU48	489
JAKMIP3	C14orf119	Q9NWQ9	480
JAKMIP3	STMP1	E0CX11	479
JAKMIP3	IQCN	Q9H0B3	470
JAKMIP3	PTK2	Q05397	468
JAKMIP3	LRRC27	Q9C0I9	431
JAKMIP3	TYK2	P29597	430
JAKMIP3	GABBR2	O75899	424
JAKMIP3	PLAC9	Q5JTB6	420
JAKMIP3	OR1J4	Q8NGS1	418
JAKMIP3	GOLGA6L7	A0A1B0GV03	417
JAKMIP3	PPP4R4	Q6NUP7	398
JAKMIP3	PYROXD1	Q8WU10	397

IntAct

8 interactions, top by confidence:

A	B	Type	Score
RYBP	PIPSL	psi-mi:“MI:0914”(association)	0.350
RYBP	FAM186A	psi-mi:“MI:0914”(association)	0.350
RIMS1	KIF2A	psi-mi:“MI:0914”(association)	0.350
HCN1	POTEF	psi-mi:“MI:0914”(association)	0.350
EPHA4	JAKMIP3	psi-mi:“MI:0915”(physical association)	0.000
NRIP1	JAKMIP3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (6): JAKMIP3 (Affinity Capture-RNA), JAKMIP3 (Affinity Capture-MS), JAKMIP3 (Two-hybrid), JAKMIP3 (Cross-Linking-MS (XL-MS)), JAKMIP3 (Cross-Linking-MS (XL-MS)), JAKMIP3 (Affinity Capture-MS)

ESM2 similar proteins: A0A287B8J2, A6QR54, A8IQT2, A8WUP2, C5E2E7, C9ZN16, G5ECG0, O08788, O16844, O48791, O55156, P13496, P28023, P35458, P45970, P54623, Q01397, Q14203, Q17695, Q23529, Q292S8, Q2KN93, Q2KN94, Q2KN95, Q2KN96, Q2KN97, Q2KN98, Q2KN99, Q2KNA0, Q2KNA1, Q3SWS9, Q585H6, Q5B993, Q5DTN8, Q5M775, Q5SXY1, Q5VZ66, Q69YQ0, Q6PCJ1, Q75EN7

Diamond homologs: A6QR54, Q3SWS9, Q5DTN8, Q5VZ66, Q8BVL9, Q96AA8, Q96N16

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

154 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	138
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

4429 predictions. Top by Δscore:

Variant	Effect	Δscore
10:132104939:GCAAG:G	donor_gain	1.0000
10:132104940:CAAG:C	donor_loss	1.0000
10:132104941:AAG:A	donor_loss	1.0000
10:132104942:AGG:A	donor_loss	1.0000
10:132104943:GGTG:G	donor_loss	1.0000
10:132104944:GTGG:G	donor_loss	1.0000
10:132104945:T:G	donor_loss	1.0000
10:132117570:GGCTG:G	donor_gain	1.0000
10:132117571:GCTG:G	donor_gain	1.0000
10:132117571:GCTGG:G	donor_gain	1.0000
10:132117572:CTGGT:C	donor_loss	1.0000
10:132117573:TGG:T	donor_loss	1.0000
10:132117574:GGTA:G	donor_loss	1.0000
10:132117575:G:GG	donor_gain	1.0000
10:132117575:G:T	donor_loss	1.0000
10:132117576:T:A	donor_loss	1.0000
10:132133520:G:GT	donor_gain	1.0000
10:132133520:G:T	donor_gain	1.0000
10:132133523:GCCCT:G	donor_gain	1.0000
10:132133528:G:GG	donor_gain	1.0000
10:132135036:TTTA:T	acceptor_loss	1.0000
10:132135037:TTA:T	acceptor_loss	1.0000
10:132135038:TAG:T	acceptor_loss	1.0000
10:132135039:A:AC	acceptor_loss	1.0000
10:132135039:A:AG	acceptor_gain	1.0000
10:132135040:G:GA	acceptor_gain	1.0000
10:132135143:G:GT	donor_gain	1.0000
10:132135151:GAA:G	donor_gain	1.0000
10:132135152:A:T	donor_gain	1.0000
10:132135157:GCTG:G	donor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000014807 (10:132094439 C>T), RS1000031580 (10:132085197 C>G), RS1000034852 (10:132179396 T>C), RS1000045541 (10:132100727 G>A), RS1000046577 (10:132115443 T>C,G), RS1000078017 (10:132075215 A>G), RS1000099516 (10:132146289 C>T), RS1000120555 (10:132183286 T>C), RS1000141176 (10:132148661 C>T), RS1000143664 (10:132109494 G>T), RS1000177594 (10:132174099 T>C), RS1000179508 (10:132171395 C>T), RS1000190210 (10:132107286 G>T), RS1000210581 (10:132111528 G>A,C), RS1000216354 (10:132063386 G>T)

Disease associations

OMIM: gene MIM:611198 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST001737_28	Chronic obstructive pulmonary disease-related biomarkers	4.000000e-06
GCST007158_1	Refractive astigmatism	3.000000e-06
GCST010988_456	Adult body size	6.000000e-12

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004810	interleukin-6 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	affects methylation, decreases expression, decreases methylation	3
sodium arsenite	decreases methylation, increases expression	2
Benzo(a)pyrene	decreases methylation, affects methylation	2
Lead	increases expression, affects expression	2
bisphenol A	decreases methylation	1
terbufos	increases methylation	1
benzo(e)pyrene	decreases methylation	1
aflatoxin B2	decreases methylation	1
abrine	decreases expression	1
Sunitinib	decreases expression	1
Amiodarone	increases expression	1
Arsenic	affects methylation	1
Benzene	increases expression	1
Diazinon	increases methylation	1
Fonofos	increases methylation	1
Melphalan	decreases expression	1
Methapyrilene	decreases methylation	1
Niclosamide	increases expression	1
Parathion	increases methylation	1
Tobacco Smoke Pollution	increases expression	1
Valproic Acid	increases methylation	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.