JHY

Summary

JHY (junctional cadherin complex regulator, HGNC:26288) is a protein-coding gene on chromosome 11q24.1, encoding Jhy protein homolog (Q6NUN7). Required for the normal development of cilia in brain ependymal cells lining the ventricular surfaces.

Predicted to be involved in axoneme assembly and brain development. Predicted to act upstream of or within several processes, including cerebrospinal fluid circulation; motile cilium assembly; and regulation of establishment of planar polarity. Predicted to be located in extracellular region.

Source: NCBI Gene 79864 — RefSeq curated summary.

At a glance

• GWAS associations: 12
• Clinical variants (ClinVar): 18 total
• MANE Select transcript: NM_024806

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26288
Approved symbol	JHY
Name	junctional cadherin complex regulator
Location	11q24.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ23554
Ensembl gene	ENSG00000109944
Ensembl biotype	protein_coding
OMIM	617594
Entrez	79864

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 13 protein_coding, 1 retained_intron

ENST00000227349, ENST00000307257, ENST00000531316, ENST00000534362, ENST00000909267, ENST00000956067, ENST00000956068, ENST00000956069, ENST00000956070, ENST00000956071, ENST00000956072, ENST00000956073, ENST00000956074, ENST00000956075

RefSeq mRNA: 5 — MANE Select: NM_024806 NM_001363087, NM_001363088, NM_001363089, NM_024806, NM_199124

CCDS: CCDS8438, CCDS8439

Canonical transcript exons

ENST00000227349 — 9 exons

Exon	Start	End
ENSE00001093401	122957363	122957491
ENSE00001093402	122956496	122956576
ENSE00001134232	122959248	122963862
ENSE00001134253	122885761	122886193
ENSE00001162873	122946498	122946792
ENSE00001162880	122934420	122935075
ENSE00001162886	122924897	122925010
ENSE00001162892	122903925	122904444
ENSE00001345846	122882759	122882972

Expression profiles

Bgee: expression breadth ubiquitous, 220 present calls, max score 87.78.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1970 / max 44.2063, expressed in 57 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
117267	0.1853	55
206482	0.0116	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	87.78	gold quality
secondary oocyte	CL:0000655	87.17	gold quality
choroid plexus epithelium	UBERON:0003911	86.26	gold quality
left testis	UBERON:0004533	85.63	gold quality
oocyte	CL:0000023	85.15	gold quality
right testis	UBERON:0004534	85.15	gold quality
epithelium of bronchus	UBERON:0002031	84.98	gold quality
testis	UBERON:0000473	84.27	gold quality
bronchus	UBERON:0002185	83.62	gold quality
sperm	CL:0000019	83.47	gold quality
buccal mucosa cell	CL:0002336	82.20	silver quality
male germ cell	CL:0000015	81.88	gold quality
mucosa of paranasal sinus	UBERON:0005030	80.85	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.95	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	77.86	gold quality
calcaneal tendon	UBERON:0003701	77.70	gold quality
right uterine tube	UBERON:0001302	77.10	gold quality
islet of Langerhans	UBERON:0000006	75.71	gold quality
pigmented layer of retina	UBERON:0001782	74.41	gold quality
tendon	UBERON:0000043	74.40	gold quality
cortical plate	UBERON:0005343	74.37	gold quality
sural nerve	UBERON:0015488	74.36	gold quality
adult organism	UBERON:0007023	73.98	gold quality
lower esophagus muscularis layer	UBERON:0035833	73.81	gold quality
lower esophagus	UBERON:0013473	73.75	gold quality
tibial nerve	UBERON:0001323	72.99	gold quality
pituitary gland	UBERON:0000007	72.78	gold quality
ventricular zone	UBERON:0003053	72.69	gold quality
adenohypophysis	UBERON:0002196	72.50	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	72.11	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.51

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting JHY, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-3667-3P	99.99	67.17	1636
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-6875-3P	99.82	70.26	2983
HSA-MIR-9851-3P	99.63	69.68	1110
HSA-MIR-3682-3P	99.58	67.63	865
HSA-MIR-593-5P	99.34	69.50	965
HSA-MIR-183-5P	99.31	72.27	1164
HSA-MIR-29A-5P	99.08	68.59	1813
HSA-MIR-384	98.71	67.34	1229
HSA-MIR-15A-3P	97.47	65.08	527
HSA-MIR-6736-3P	96.98	65.22	1342
HSA-MIR-1295B-3P	96.68	66.11	276
HSA-MIR-3690	96.44	65.18	737
HSA-MIR-3619-3P	95.59	65.99	428
HSA-MIR-184	94.24	64.40	152
HSA-MIR-4804-5P	91.83	65.35	105

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	jhy	ENSDARG00000068982
mus_musculus	Jhy	ENSMUSG00000032023
rattus_norvegicus	Jhy	ENSRNOG00000008138

Protein

Protein identifiers

Jhy protein homolog — Q6NUN7 (reviewed: Q6NUN7)

All UniProt accessions (1): Q6NUN7

UniProt curated annotations — full annotation on UniProt →

Function. Required for the normal development of cilia in brain ependymal cells lining the ventricular surfaces.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6NUN7-1	1	yes
Q6NUN7-2	2

RefSeq proteins (5): NP_001350016, NP_001350017, NP_001350018, NP_079082, NP_954575 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR027968	JHY	Family

Pfam: PF15261

UniProt features (17 total): compositionally biased region 8, region of interest 4, splice variant 2, chain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6NUN7-F1	51.82	0.06

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 95 (showing top): GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_CILIUM_ORGANIZATION, GOBP_CILIUM_MOVEMENT, GOBP_ORGANELLE_ASSEMBLY, GOBP_MICROTUBULE_BUNDLE_FORMATION, GOBP_HEAD_DEVELOPMENT, GOBP_MORPHOGENESIS_OF_A_POLARIZED_EPITHELIUM, GOBP_MOTILE_CILIUM_ASSEMBLY, GOBP_CELL_PROJECTION_ORGANIZATION, VECCHI_GASTRIC_CANCER_EARLY_DN, GOBP_AXONEME_ASSEMBLY, GOBP_TISSUE_MORPHOGENESIS, TAATTA_CHX10_01

GO Biological Process (8): brain development (GO:0007420), cell differentiation (GO:0030154), axoneme assembly (GO:0035082), motile cilium assembly (GO:0044458), establishment of localization in cell (GO:0051649), regulation of establishment of planar polarity (GO:0090175), cerebrospinal fluid circulation (GO:0090660), cell projection organization (GO:0030030)

GO Molecular Function (0):

GO Cellular Component (1): extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cilium assembly	2
central nervous system development	1
animal organ development	1
head development	1
cellular developmental process	1
microtubule bundle formation	1
cellular component assembly	1
establishment of localization	1
cellular localization	1
establishment of planar polarity	1
regulation of animal organ morphogenesis	1
epithelial cilium movement involved in extracellular fluid movement	1
nervous system process	1
cellular component organization	1
cellular anatomical structure	1

Protein interactions and networks

STRING

282 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
JHY	RSPH9	Q9H1X1	471
JHY	DNAAF11	Q86X45	469
JHY	ULK4	Q96C45	459
JHY	ZMYND10	O75800	431
JHY	OR13A1	Q8NGR1	431
JHY	OR5P3	Q8WZ94	419
JHY	MINDY1	Q8N5J2	405
JHY	ZNF394	Q53GI3	403
JHY	ZNF835	Q9Y2P0	400
JHY	CCDC39	Q9UFE4	398
JHY	ZNF483	Q8TF39	378
JHY	ZNF682	O95780	377
JHY	SLC25A35	Q3KQZ1	375
JHY	ZNF549	Q6P9A3	370
JHY	MOGAT3	Q86VF5	367

IntAct

4 interactions, top by confidence:

A	B	Type	Score
JHY	LRRK2	psi-mi:“MI:0407”(direct interaction)	0.440
JHY	DAPK1	psi-mi:“MI:0407”(direct interaction)	0.440
SRPK1	JHY	psi-mi:“MI:0217”(phosphorylation reaction)	0.440

BioGRID (10): C11orf63 (Reconstituted Complex), C11orf63 (Reconstituted Complex), C11orf63 (Affinity Capture-RNA), HIST1H3A (Cross-Linking-MS (XL-MS)), C11orf63 (Cross-Linking-MS (XL-MS)), C11orf63 (Reconstituted Complex), C11orf63 (Biochemical Activity), APP (Reconstituted Complex), C11orf63 (Biochemical Activity), C11orf63 (Biochemical Activity)

ESM2 similar proteins: A0JNH1, A6NFA0, A6NGY1, A6QNQ6, A7YY35, D3Z1D3, D3Z987, E1BC15, E9Q286, E9Q3S4, M0RD54, O14513, P70347, Q05860, Q0VBV7, Q1RMX6, Q2M2Z5, Q2M3C7, Q3MHH3, Q3U0P1, Q3URK1, Q3UXL4, Q3V089, Q49AJ0, Q569L8, Q5BQN8, Q5DTT3, Q5HZI1, Q5T1N1, Q5VWN6, Q5ZK13, Q61493, Q64ET8, Q68DA7, Q6NUN7, Q6PDM4, Q6PG16, Q6ZVD7, Q711Q0, Q7TSH4

Diamond homologs: E9Q793, Q2T9M9, Q6NUN7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	4
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2154 predictions. Top by Δscore:

Variant	Effect	Δscore
11:122886193:GGTA:G	donor_loss	1.0000
11:122886194:GT:G	donor_loss	1.0000
11:122903913:T:TA	acceptor_gain	1.0000
11:122903918:T:TA	acceptor_gain	1.0000
11:122903919:G:A	acceptor_gain	1.0000
11:122925005:C:G	donor_gain	1.0000
11:122956577:G:GG	donor_gain	1.0000
11:122957487:AGAAG:A	donor_loss	1.0000
11:122957488:GAAG:G	donor_gain	1.0000
11:122957492:G:GA	donor_loss	1.0000
11:122957493:T:A	donor_loss	1.0000
11:122885755:TTTCA:T	acceptor_loss	0.9900
11:122885756:TTCA:T	acceptor_loss	0.9900
11:122885757:TCAG:T	acceptor_loss	0.9900
11:122885758:CA:C	acceptor_loss	0.9900
11:122885759:A:AG	acceptor_gain	0.9900
11:122885759:A:AT	acceptor_loss	0.9900
11:122885760:G:GA	acceptor_loss	0.9900
11:122885760:G:GG	acceptor_gain	0.9900
11:122903923:A:AG	acceptor_gain	0.9900
11:122903923:A:AT	acceptor_loss	0.9900
11:122903924:G:A	acceptor_loss	0.9900
11:122903924:G:GT	acceptor_gain	0.9900
11:122903924:GGC:G	acceptor_gain	0.9900
11:122903924:GGCA:G	acceptor_gain	0.9900
11:122904441:ACAGG:A	donor_loss	0.9900
11:122904445:G:T	donor_loss	0.9900
11:122904446:T:G	donor_loss	0.9900
11:122924895:A:AG	acceptor_gain	0.9900
11:122924896:G:GG	acceptor_gain	0.9900

AlphaMissense

5155 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:122959410:G:C	A768P	0.987
11:122959261:C:A	A718D	0.984
11:122959416:G:C	A770P	0.981
11:122959423:T:C	F772S	0.980
11:122959260:G:C	A718P	0.978
11:122959419:G:C	A771P	0.974
11:122959402:A:T	E765V	0.973
11:122959258:A:C	Y717S	0.972
11:122904357:C:A	N259K	0.971
11:122904357:C:G	N259K	0.971
11:122959381:T:C	L758P	0.970
11:122959406:A:C	K766N	0.962
11:122959406:A:T	K766N	0.962
11:122904360:G:C	K260N	0.961
11:122904360:G:T	K260N	0.961
11:122959432:T:C	L775P	0.960
11:122959403:A:C	E765D	0.959
11:122959403:A:T	E765D	0.959
11:122957393:G:C	A681P	0.958
11:122959391:A:C	R761S	0.957
11:122959391:A:T	R761S	0.957
11:122959422:T:C	F772L	0.955
11:122959424:C:A	F772L	0.955
11:122959424:C:G	F772L	0.955
11:122959258:A:G	Y717C	0.954
11:122959257:T:C	Y717H	0.953
11:122959257:T:G	Y717D	0.953
11:122959393:A:C	H762P	0.953
11:122924984:T:A	W318R	0.949
11:122924984:T:C	W318R	0.949

dbSNP variants (sampled 300 via entrez): RS1000042402 (11:122958284 G>A), RS1000055973 (11:122923100 C>A,T), RS1000141198 (11:122961334 G>T), RS1000191730 (11:122961527 A>G), RS1000208632 (11:122955009 T>C), RS1000209416 (11:122912667 G>A), RS1000239161 (11:122912889 C>A,T), RS1000244985 (11:122953078 T>C), RS1000261938 (11:122884967 T>G), RS1000297306 (11:122916636 TTTG>T,TTTGTTG), RS1000353684 (11:122948676 A>C), RS1000366646 (11:122948835 C>T), RS1000372244 (11:122891728 A>T), RS1000387587 (11:122882758 T>C), RS1000421384 (11:122906810 C>A)

Disease associations

OMIM: gene MIM:617594 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

12 associations (top):

Study	Trait	p-value
GCST003993_30	Menarche (age at onset)	7.000000e-12
GCST003994_10	Age at voice drop	2.000000e-13
GCST005867_19	Menarche (age at onset)	1.000000e-08
GCST006288_5	Heel bone mineral density	3.000000e-09
GCST007202_20	High density lipoprotein cholesterol levels	2.000000e-06
GCST007560_6	Sleep duration (long sleep)	2.000000e-08
GCST007576_342	Chronotype	4.000000e-10
GCST010989_31	Body size at age 10	4.000000e-09
GCST012226_307	Waist circumference adjusted for body mass index	1.000000e-09
GCST012227_631	Hip circumference adjusted for BMI	2.000000e-08
GCST012227_632	Hip circumference adjusted for BMI	2.000000e-13
GCST012490_250	Femur bone mineral density x serum urate levels interaction	8.000000e-09

EFO canonical traits (9, from GWAS)

EFO ID	Trait name
EFO:0004703	age at menarche
EFO:0007888	age at voice drop
EFO:0009270	heel bone mineral density
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0008328	chronotype measurement
EFO:0009819	comparative body size at age 10, self-reported
EFO:0007789	BMI-adjusted waist circumference
EFO:0008039	BMI-adjusted hip circumference
EFO:0004531	urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

19 total (human), top 19 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	2
Tobacco Smoke Pollution	affects expression, increases expression	2
Particulate Matter	increases abundance, increases expression	2
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
bisphenol A	increases expression	1
sulforaphane	increases expression	1
butyraldehyde	decreases expression	1
benzo(e)pyrene	increases methylation	1
aflatoxin B2	increases methylation	1
cupric chloride	increases expression	1
nickel sulfate	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Arsenic	increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation, increases methylation	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Doxorubicin	decreases expression	1
Methapyrilene	increases methylation	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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