KATNIP

Summary

KATNIP (katanin interacting protein, HGNC:29068) is a protein-coding gene on chromosome 16p12.1, encoding Katanin-interacting protein (O60303). May influence the stability of microtubules (MT), possibly through interaction with the MT-severing katanin complex.

This gene encodes a novel, evolutionarily conserved, ciliary protein. In human hTERT-RPE1 cells, the protein is found at the base of cilia, decorating the ciliary axoneme, and enriched at the ciliary tip. The protein binds to microtubules in vitro and regulates their stability when it is overexpressed. A null mutation in this gene has been associated with Joubert syndrome, a recessive disorder that is characterized by a distinctive mid-hindbrain and cerebellar malformation and is also often associated with wider ciliopathy symptoms. Consistently, in a serum-starvation ciliogenesis assay, human fibroblast cells derived from patients with the mutation display a reduced number of ciliated cells with abnormally long cilia.

Source: NCBI Gene 23247 — RefSeq curated summary.

At a glance

• Gene–disease (curated): ciliopathy (Definitive, ClinGen) — +2 more curated relationships
• GWAS associations: 5
• Clinical variants (ClinVar): 833 total — 20 pathogenic, 24 likely-pathogenic
• Phenotypes (HPO): 50
• MANE Select transcript: NM_015202

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29068
Approved symbol	KATNIP
Name	katanin interacting protein
Location	16p12.1
Locus type	gene with protein product
Status	Approved
Aliases	JBTS26
Ensembl gene	ENSG00000047578
Ensembl biotype	protein_coding
OMIM	616650
Entrez	23247

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 5 retained_intron, 4 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000261588, ENST00000562207, ENST00000564749, ENST00000565672, ENST00000566023, ENST00000567894, ENST00000568258, ENST00000568622, ENST00000573850, ENST00000618117, ENST00000862512

RefSeq mRNA: 1 — MANE Select: NM_015202 NM_015202

CCDS: CCDS32415

Canonical transcript exons

ENST00000261588 — 28 exons

Exon	Start	End
ENSE00000830160	27754173	27754251
ENSE00000830163	27740041	27740920
ENSE00000944676	27761413	27761590
ENSE00000944677	27766309	27766474
ENSE00000944678	27769861	27770018
ENSE00000944679	27771588	27771652
ENSE00001022224	27773099	27773209
ENSE00001022226	27776928	27777029
ENSE00001022227	27774945	27775084
ENSE00001250174	27778574	27780344
ENSE00001785949	27618425	27618501
ENSE00001789098	27573901	27573956
ENSE00002268888	27550144	27550177
ENSE00003521823	27708705	27708920
ENSE00003528429	27751719	27751924
ENSE00003536285	27699534	27699599
ENSE00003558275	27703896	27703998
ENSE00003565745	27701589	27701695
ENSE00003622499	27648604	27648735
ENSE00003636681	27721558	27721695
ENSE00003642903	27677729	27677996
ENSE00003648939	27749584	27750306
ENSE00003661239	27777881	27777969
ENSE00003662802	27681399	27681530
ENSE00003662824	27628661	27628830
ENSE00003680152	27698328	27698500
ENSE00003680761	27777610	27777770
ENSE00003689381	27631065	27631162

Expression profiles

Bgee: expression breadth ubiquitous, 251 present calls, max score 98.97.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.6807 / max 126.8765, expressed in 1780 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
153342	10.3675	1776
153343	0.3053	91
153344	0.0079	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	98.97	gold quality
bronchial epithelial cell	CL:0002328	94.25	gold quality
epithelium of bronchus	UBERON:0002031	94.03	gold quality
bronchus	UBERON:0002185	93.63	gold quality
left lobe of thyroid gland	UBERON:0001120	91.81	gold quality
right lobe of thyroid gland	UBERON:0001119	91.75	gold quality
thyroid gland	UBERON:0002046	91.16	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	89.26	gold quality
pituitary gland	UBERON:0000007	88.78	gold quality
nasal cavity epithelium	UBERON:0005384	88.31	gold quality
metanephros cortex	UBERON:0010533	88.29	gold quality
adenohypophysis	UBERON:0002196	87.97	gold quality
pancreatic ductal cell	CL:0002079	87.09	silver quality
lower esophagus mucosa	UBERON:0035834	87.00	gold quality
apex of heart	UBERON:0002098	86.97	gold quality
body of pancreas	UBERON:0001150	86.61	gold quality
esophagus mucosa	UBERON:0002469	86.22	gold quality
pigmented layer of retina	UBERON:0001782	86.07	gold quality
retina	UBERON:0000966	86.05	gold quality
body of stomach	UBERON:0001161	85.67	gold quality
skin of leg	UBERON:0001511	85.59	gold quality
sural nerve	UBERON:0015488	85.30	gold quality
stomach	UBERON:0000945	85.00	gold quality
ileal mucosa	UBERON:0000331	84.87	gold quality
skin of abdomen	UBERON:0001416	84.87	gold quality
minor salivary gland	UBERON:0001830	84.82	gold quality
lateral globus pallidus	UBERON:0002476	84.82	gold quality
left testis	UBERON:0004533	84.74	gold quality
granulocyte	CL:0000094	84.71	gold quality
transverse colon	UBERON:0001157	84.54	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.36

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

67 targeting KATNIP, 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-3134	100.00	66.43	777
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-448	99.79	72.37	2103
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-6887-3P	99.66	67.83	1778
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-642A-5P	99.51	65.10	1152
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-4667-3P	99.26	65.45	1608
HSA-MIR-4685-5P	99.25	65.99	1563
HSA-MIR-6837-5P	99.25	65.47	1632
HSA-MIR-100-3P	99.20	67.33	672
HSA-MIR-8052	99.17	65.01	719
HSA-MIR-3125	99.14	68.49	2269
HSA-MIR-661	99.09	65.94	2062
HSA-MIR-6506-5P	99.04	65.66	1386
HSA-MIR-1909-3P	99.03	66.56	1662
HSA-MIR-3916	98.99	68.04	2155
HSA-MIR-6859-5P	98.99	68.07	2049

Literature-anchored findings (GeneRIF, showing 7)

• KIAA0056 (also known as mouse MGC31549) is a strong candidate gene for retinitis pigmentosa, RP22 (human 16p12.3-p12.1). Conclusion is based on a massive expression data set for mouse (103 strains in Genenetwork.org) and joint analysis of RetNet database. (PMID:19727342)
• KIAA0556 mutation identified in patients with Joubert syndrome. KIAA0556 binds to microtubules, p60/p80 katanins and genetically interacts with ARL13B. (PMID:26714646)
• Whole exome sequencing in a multiplex consanguineous family from India revealed a KIAA0556 homozygous single base pair deletion mutation (c.4420del; p.Met1474Cysfs*11). Knockdown of the gene in zebrafish resulted in a ciliopathy phenotype, rescued by co-injection of wildtype cDNA (PMID:27245168)
• homozygous truncating mutations in both ADGRG1/GPR56 and KIAA0556 are found in brothers displaying an overlap of polymicrogyria, hydrocephalus, and Joubert syndrome (PMID:30982090)
• Pathogenic germline variants of KIAA0556 associated with hypothalamic hamartoma were found. (PMID:31197031)
• Co-occurrence of mutations in KIF7 and KIAA0556 in Joubert syndrome with ocular coloboma, pituitary malformation and growth hormone deficiency: a case report and literature review. (PMID:32164589)
• The Scaffold Protein KATNIP Enhances CILK1 Control of Primary Cilia. (PMID:37665596)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	katnip	ENSDARG00000092347
danio_rerio	si:dkey-161j23.7	ENSDARG00000092882
danio_rerio	si:dkey-161j23.5	ENSDARG00000094441
mus_musculus	Katnip	ENSMUSG00000032743
rattus_norvegicus	Katnip	ENSRNOG00000016635
caenorhabditis_elegans	K04F10.2	WBGENE00019395

Protein

Protein identifiers

Katanin-interacting protein — O60303 (reviewed: O60303)

All UniProt accessions (4): A0A087X098, O60303, H3BNJ6, H3BPM2

UniProt curated annotations — full annotation on UniProt →

Function. May influence the stability of microtubules (MT), possibly through interaction with the MT-severing katanin complex.

Subunit / interactions. Interacts with microtubules. Interacts with 4 subunits of the katanin complex: KATNA1, KATNAL1, KATNB1 and KATNBL1.

Subcellular location. Cytoplasm. Cytoskeleton. Cilium axoneme. Cilium basal body.

Disease relevance. Joubert syndrome 26 (JBTS26) [MIM:616784] A form of Joubert syndrome, a disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy, renal disease, liver fibrosis, and polydactyly. JBTS26 inheritance is autosomal recessive. The disease is caused by variants affecting the gene represented in this entry.

RefSeq proteins (1): NP_056017* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026704	KATNIP	Family
IPR027859	KATNIP_dom	Domain

Pfam: PF14652

UniProt features (28 total): region of interest 9, sequence variant 8, compositionally biased region 6, modified residue 3, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O60303-F1	58.93	0.23

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 (3): 453, 660, 691

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 232 (showing top): MODULE_255, MODULE_317, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_NEGATIVE_REGULATION_OF_ORGANELLE_ASSEMBLY, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, MODULE_205, GOBP_CILIUM_ORGANIZATION, GOBP_CILIUM_MOVEMENT, GOBP_ORGANELLE_ASSEMBLY, GOBP_NEGATIVE_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_REGULATION_OF_CILIUM_ASSEMBLY, GOBP_MOTILE_CILIUM_ASSEMBLY

GO Biological Process (2): cerebrospinal fluid circulation (GO:0090660), negative regulation of motile cilium assembly (GO:1905504)

GO Molecular Function (3): microtubule binding (GO:0008017), tubulin binding (GO:0015631), intraciliary transport particle B binding (GO:0120170)

GO Cellular Component (12): obsolete extracellular space (GO:0005615), nucleoplasm (GO:0005654), plasma membrane (GO:0005886), cilium (GO:0005929), axoneme (GO:0005930), centriolar satellite (GO:0034451), ciliary basal body (GO:0036064), ciliary base (GO:0097546), 9+2 motile cilium (GO:0097729), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	6
cilium	2
epithelial cilium movement involved in extracellular fluid movement	1
nervous system process	1
motile cilium assembly	1
negative regulation of cilium assembly	1
regulation of motile cilium assembly	1
tubulin binding	1
cytoskeletal protein binding	1
protein-containing complex binding	1
nuclear lumen	1
membrane	1
cell periphery	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cytoskeleton	1
microtubule	1
ciliary plasm	1
centrosome	1
microtubule organizing center	1
ciliary transition zone	1
ciliary transition fiber	1
radial spoke	1
motile cilium	1
inner dynein arm	1
outer dynein arm	1
axonemal central pair	1
axonemal doublet microtubule	1
intracellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

1130 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KATNIP	CEP104	O60308	690
KATNIP	KATNB1	Q9BVA0	605
KATNIP	KIF7	Q2M1P5	555
KATNIP	ARMC9	Q7Z3E5	540
KATNIP	CSPP1	Q1MSJ5	513
KATNIP	TMEM67	Q5HYA8	491
KATNIP	ARL13B	Q3SXY8	469
KATNIP	CC2D2A	Q9P2K1	454
KATNIP	CEP41	Q9BYV8	452
KATNIP	DERL2	Q9GZP9	447
KATNIP	LRRC63	Q05C16	446
KATNIP	CEP97	Q8IW35	441
KATNIP	KIAA0586	Q9BVV6	435
KATNIP	KATNAL2	Q8IYT4	434
KATNIP	RECQL5	O94762	425

IntAct

16 interactions, top by confidence:

A	B	Type	Score
KATNIP	MAK	psi-mi:“MI:0914”(association)	0.730
KATNBL1	KATNIP	psi-mi:“MI:0915”(physical association)	0.480
IFT88	KATNIP	psi-mi:“MI:0915”(physical association)	0.480
TBC1D4	KATNIP	psi-mi:“MI:0915”(physical association)	0.370
LLGL2	RBBP6	psi-mi:“MI:0914”(association)	0.350
Tmed2		psi-mi:“MI:0914”(association)	0.350
Vps28	UMAD1	psi-mi:“MI:0914”(association)	0.350
KIF2A	EIF3F	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
KATNIP		psi-mi:“MI:0914”(association)	0.350
MAK	CNOT1	psi-mi:“MI:0914”(association)	0.350
CILK1	MAST4	psi-mi:“MI:0914”(association)	0.350
MAK	KATNIP	psi-mi:“MI:0915”(physical association)	0.000
KATNIP	CILK1	psi-mi:“MI:0915”(physical association)	0.000
KATNIP	prmB	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (16): KIAA0556 (Affinity Capture-MS), KIAA0556 (Affinity Capture-MS), KIAA0556 (Affinity Capture-MS), KIAA0556 (Affinity Capture-MS), KIAA0556 (Affinity Capture-MS), KIAA0556 (Affinity Capture-MS), ICK (Affinity Capture-MS), KIAA0556 (Affinity Capture-RNA), KIAA0556 (Affinity Capture-RNA), KIAA0556 (Affinity Capture-MS), KIAA0556 (Affinity Capture-MS), KIAA0556 (Affinity Capture-MS), KIAA0556 (Proximity Label-MS), KIAA0556 (Proximity Label-MS), KIAA0556 (Affinity Capture-MS)

ESM2 similar proteins: A0JNF3, A1L253, A2AHC3, A3KP40, A5PLN7, A5WUN7, A6H5Y1, B1AXH1, B2GUZ2, D3Z8E6, E9PV87, E9Q309, H6D7E6, O14513, O60303, P0CAX8, P28290, Q14B48, Q1G7G9, Q2KHM9, Q32LN6, Q49A88, Q566N9, Q5HYW2, Q5PQL8, Q5REU9, Q5T5Y3, Q5VT06, Q60664, Q66H35, Q66MI6, Q6A000, Q6AYP4, Q6NSV7, Q6NXP0, Q6ZRS4, Q6ZVD7, Q80VP2, Q8BJS7, Q8CB14

Diamond homologs: O44770, O60303, Q8C753, Q5XK85

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	20
Likely pathogenic	24
Uncertain significance	405
Likely benign	263
Benign	57

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1298658	NM_015202.5(KATNIP):c.4240del (p.Tyr1414fs)	Pathogenic
1682065	NM_015202.5(KATNIP):c.3259C>T (p.Arg1087Ter)	Pathogenic
1960397	NM_015202.5(KATNIP):c.4291dup (p.Ile1431fs)	Pathogenic
1967693	NM_015202.5(KATNIP):c.4572dup (p.Val1525fs)	Pathogenic
1982866	NM_015202.5(KATNIP):c.808del (p.Ser270fs)	Pathogenic
2426096	NC_000016.9:g.(?27712890)(27713036_?)del	Pathogenic
2831377	NM_015202.5(KATNIP):c.3626dup (p.Ile1210fs)	Pathogenic
3009140	NM_015202.5(KATNIP):c.1102_1105dup (p.Pro369fs)	Pathogenic
3112895	NM_015202.5(KATNIP):c.4243del (p.Tyr1415fs)	Pathogenic
3233461	NC_000016.9:g.(27561499_27585221)_(27585278_27629745)del	Pathogenic
3243648	NC_000016.9:g.(?27585202)(27585297_?)del	Pathogenic
3243650	NC_000016.9:g.(?27659905)(27689337_?)del	Pathogenic
3251831	NM_015202.5(KATNIP):c.19C>T (p.Arg7Ter)	Pathogenic
3660624	NM_015202.5(KATNIP):c.1628G>A (p.Trp543Ter)	Pathogenic
3700761	NM_015202.5(KATNIP):c.4531C>T (p.Arg1511Ter)	Pathogenic
3708847	NM_015202.5(KATNIP):c.16_17del (p.Leu6fs)	Pathogenic
3895621	NM_015202.5(KATNIP):c.3584del (p.Pro1195fs)	Pathogenic
4716846	NM_015202.5(KATNIP):c.4295_4296del (p.Pro1432fs)	Pathogenic
4847907	NM_015202.5(KATNIP):c.319C>T (p.Arg107Ter)	Pathogenic
489396	NM_015202.5(KATNIP):c.4420del (p.Met1474fs)	Pathogenic
1327056	NM_015202.5(KATNIP):c.2959del (p.Asp987fs)	Likely pathogenic
1334634	NM_015202.5(KATNIP):c.4133+1G>A	Likely pathogenic
2053053	NM_015202.5(KATNIP):c.1389+2T>C	Likely pathogenic
218948	NM_015202.5(KATNIP):c.2674C>T (p.Gln892Ter)	Likely pathogenic
2431062	NM_015202.5(KATNIP):c.274_275del (p.Phe92fs)	Likely pathogenic
2443382	NM_015202.5(KATNIP):c.2960del (p.Asp987fs)	Likely pathogenic
2443383	NM_015202.5(KATNIP):c.2914C>A (p.Pro972Thr)	Likely pathogenic
2501211	NM_015202.5(KATNIP):c.922C>T (p.Gln308Ter)	Likely pathogenic
2629526	NM_015202.5(KATNIP):c.1387G>T (p.Glu463Ter)	Likely pathogenic
2690629	NM_015202.5(KATNIP):c.3632-1G>C	Likely pathogenic

SpliceAI

5595 predictions. Top by Δscore:

Variant	Effect	Δscore
16:27618540:G:GT	donor_gain	1.0000
16:27618543:G:GG	donor_gain	1.0000
16:27628655:TTTCA:T	acceptor_loss	1.0000
16:27628656:TTCA:T	acceptor_loss	1.0000
16:27628658:CA:C	acceptor_loss	1.0000
16:27628659:A:C	acceptor_loss	1.0000
16:27628659:AG:A	acceptor_gain	1.0000
16:27628660:GG:G	acceptor_gain	1.0000
16:27628660:GGAT:G	acceptor_gain	1.0000
16:27628776:A:T	donor_gain	1.0000
16:27628828:ACGG:A	donor_loss	1.0000
16:27628830:GGTG:G	donor_loss	1.0000
16:27628831:G:GG	donor_gain	1.0000
16:27628831:GT:G	donor_loss	1.0000
16:27628832:T:G	donor_loss	1.0000
16:27631134:G:GG	donor_gain	1.0000
16:27677715:T:TA	acceptor_gain	1.0000
16:27677716:G:A	acceptor_gain	1.0000
16:27677724:TGCAG:T	acceptor_loss	1.0000
16:27677725:GCAGG:G	acceptor_loss	1.0000
16:27677726:CA:C	acceptor_loss	1.0000
16:27677727:AG:A	acceptor_gain	1.0000
16:27677728:GG:G	acceptor_gain	1.0000
16:27677728:GGA:G	acceptor_gain	1.0000
16:27677728:GGAGC:G	acceptor_gain	1.0000
16:27677937:G:GT	donor_gain	1.0000
16:27677997:G:GG	donor_gain	1.0000
16:27678002:C:G	donor_gain	1.0000
16:27681520:G:GT	donor_gain	1.0000
16:27681525:GCTCC:G	donor_gain	1.0000

AlphaMissense

10650 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:27750102:T:A	W1048R	0.999
16:27750102:T:C	W1048R	0.999
16:27750191:C:A	N1077K	0.999
16:27750191:C:G	N1077K	0.999
16:27775058:T:A	W1475R	0.999
16:27775058:T:C	W1475R	0.999
16:27749938:T:C	L993P	0.998
16:27766352:T:A	W1285R	0.998
16:27766352:T:C	W1285R	0.998
16:27766441:C:A	N1314K	0.998
16:27766441:C:G	N1314K	0.998
16:27773153:T:C	L1418P	0.998
16:27776990:T:A	N1504K	0.998
16:27776990:T:G	N1504K	0.998
16:27749932:T:A	V991D	0.997
16:27750106:T:C	L1049P	0.997
16:27750199:A:T	K1080I	0.997
16:27750200:A:C	K1080N	0.997
16:27750200:A:T	K1080N	0.997
16:27750264:T:C	F1102L	0.997
16:27750266:T:A	F1102L	0.997
16:27750266:T:G	F1102L	0.997
16:27751749:T:C	F1126S	0.997
16:27773125:A:C	S1409R	0.997
16:27773127:C:A	S1409R	0.997
16:27773127:C:G	S1409R	0.997
16:27773150:G:A	G1417D	0.997
16:27774954:C:A	A1440D	0.997
16:27774965:A:C	S1444R	0.997
16:27774967:C:A	S1444R	0.997

dbSNP variants (sampled 300 via entrez): RS1000021349 (16:27593446 C>T), RS1000027366 (16:27700508 A>G), RS1000074470 (16:27600065 C>T), RS1000086658 (16:27677474 C>A,G), RS1000092572 (16:27772897 A>G), RS1000117405 (16:27737854 G>A,C), RS1000155716 (16:27652014 C>G,T), RS1000173613 (16:27569331 G>A), RS1000176485 (16:27559967 C>A,T), RS1000200767 (16:27618346 C>T), RS1000204672 (16:27569042 T>C), RS1000208386 (16:27707575 G>A), RS1000228540 (16:27696895 A>T), RS1000236612 (16:27701765 G>T), RS1000245921 (16:27702893 G>A,T)

Disease associations

OMIM: gene MIM:616650 | disease phenotypes: MIM:616784, MIM:213300

GenCC curated gene-disease

Disease	Classification	Inheritance
Joubert syndrome 26	Strong	Autosomal recessive
Joubert syndrome	Supportive	Autosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
ciliopathy	Definitive	AR

Mondo (4): Joubert syndrome 26 (MONDO:0014771), ciliopathy (MONDO:0005308), Joubert syndrome (MONDO:0018772), Joubert syndrome 1 (MONDO:0008944)

Orphanet (2): Isolated Joubert syndrome (Orphanet:475), Ciliopathy (Orphanet:363250)

HPO phenotypes

50 total (30 of 50 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000054	Micropenis
HP:0000175	Cleft palate
HP:0000202	Orofacial cleft
HP:0000238	Hydrocephalus
HP:0000276	Long face
HP:0000316	Hypertelorism
HP:0000369	Low-set ears
HP:0000426	Prominent nasal bridge
HP:0000463	Anteverted nares
HP:0000486	Strabismus
HP:0000508	Ptosis
HP:0000612	Iris coloboma
HP:0000639	Nystagmus
HP:0000657	Oculomotor apraxia
HP:0000824	Decreased response to growth hormone stimulation test
HP:0000864	Abnormality of the hypothalamus-pituitary axis
HP:0000871	Panhypopituitarism
HP:0001161	Hand polydactyly
HP:0001249	Intellectual disability
HP:0001250	Seizure
HP:0001251	Ataxia
HP:0001252	Hypotonia
HP:0001263	Global developmental delay
HP:0001288	Gait disturbance
HP:0001290	Generalized hypotonia
HP:0001320	Cerebellar vermis hypoplasia
HP:0001337	Tremor
HP:0001696	Situs inversus totalis
HP:0001829	Foot polydactyly

GWAS associations

5 associations (top):

Study	Trait	p-value
GCST005024_31	Pursuit maintenance gain	9.000000e-06
GCST009200_13	Whole brain grey matter density	3.000000e-07
GCST009276_1	Response to placebo treatment in childhood asthma (FVC change)	1.000000e-06
GCST009276_2	Response to placebo treatment in childhood asthma (FVC change)	1.000000e-06
GCST009276_9	Response to placebo treatment in childhood asthma (FVC change)	4.000000e-06

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0008433	pursuit maintenance gain measurement
EFO:0010306	Grey matter density measurement
EFO:0008344	response to placebo
EFO:0010339	FVC change measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

33 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases methylation, increases expression, affects cotreatment	2
Benzo(a)pyrene	affects methylation, decreases expression	2
FR900359	decreases phosphorylation	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
butyraldehyde	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
coumarin	decreases phosphorylation	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Acetaminophen	increases expression	1
Caffeine	decreases phosphorylation	1
Catechin	affects cotreatment, increases expression	1
Coumestrol	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1
Methotrexate	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Quercetin	increases expression	1
Smoke	decreases expression	1
Thiram	increases expression	1
1-Methyl-3-isobutylxanthine	affects cotreatment, increases expression	1

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_E2AB	HAP1 KIAA0556 (-) 1	Cancer cell line	Male
CVCL_E2AC	HAP1 KIAA0556 (-) 2	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00873678	Not specified	COMPLETED	Assessment of the Prevalence of Genes AHI1, NPHP1 and CEP290 in Joubert Syndrome
NCT01401998	Not specified	RECRUITING	ARPKD Database Study
NCT04874909	Not specified	COMPLETED	Classification, Functional Stratification and Biomarkers in Ciliopathy (CILLICORIRCM)
NCT00068224	Not specified	COMPLETED	Clinical and Molecular Investigations Into Ciliopathies