CEP83

Summary

CEP83 (centrosomal protein 83, HGNC:17966) is a protein-coding gene on chromosome 12q22, encoding Centrosomal protein of 83 kDa (Q9Y592). Component of the distal appendage region of the centriole involved in the initiation of primary cilium assembly.

The protein encoded by this gene is a centriolar protein involved in primary cilium assembly. Defects in this gene have been associated with infantile nephronophthisis and intellectual disability.

Source: NCBI Gene 51134 — RefSeq curated summary.

At a glance

• Gene–disease (curated): nephronophthisis 18 (Definitive, GenCC) — +1 more curated relationship
• GWAS associations: 9
• Clinical variants (ClinVar): 605 total — 37 pathogenic, 7 likely-pathogenic
• Phenotypes (HPO): 13
• MANE Select transcript: NM_016122

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:17966
Approved symbol	CEP83
Name	centrosomal protein 83
Location	12q22
Locus type	gene with protein product
Status	Approved
Aliases	NY-REN-58, NPHP18
Ensembl gene	ENSG00000173588
Ensembl biotype	protein_coding
OMIM	615847
Entrez	51134

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 11 protein_coding, 5 protein_coding_CDS_not_defined, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000339839, ENST00000397809, ENST00000546527, ENST00000546587, ENST00000546783, ENST00000547232, ENST00000547575, ENST00000549352, ENST00000550328, ENST00000551078, ENST00000551250, ENST00000551596, ENST00000552632, ENST00000861191, ENST00000914421, ENST00000914422, ENST00000914423, ENST00000949376, ENST00000949377

RefSeq mRNA: 13 — MANE Select: NM_016122 NM_001042399, NM_001346457, NM_001346458, NM_001346459, NM_001346460, NM_001346461, NM_001346462, NM_001368037, NM_001368038, NM_001368039, NM_001368040, NM_001368041, NM_016122

CCDS: CCDS41820, CCDS86323

Canonical transcript exons

ENST00000397809 — 17 exons

Exon	Start	End
ENSE00001197682	94331700	94331829
ENSE00001197687	94333482	94333639
ENSE00001197692	94335589	94335664
ENSE00001197698	94367794	94367943
ENSE00001197704	94368057	94368201
ENSE00001197710	94369922	94370036
ENSE00001787056	94412318	94412591
ENSE00002316477	94435275	94435327
ENSE00002328721	94307698	94308917
ENSE00003471629	94378791	94379042
ENSE00003475582	94400850	94400981
ENSE00003585213	94411697	94411847
ENSE00003629350	94312914	94313017
ENSE00003636187	94309918	94310107
ENSE00003672912	94375886	94376017
ENSE00003751864	94403170	94403262
ENSE00003890810	94459557	94459867

Expression profiles

Bgee: expression breadth ubiquitous, 233 present calls, max score 95.82.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.6829 / max 137.5056, expressed in 1580 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
132692	3.0232	1287
132694	1.2469	681
132693	1.1552	653
132691	1.0764	626
132695	0.1578	57
132688	0.0125	6
132687	0.0066	3
132689	0.0043	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	95.82	gold quality
calcaneal tendon	UBERON:0003701	92.52	gold quality
sural nerve	UBERON:0015488	91.49	gold quality
right testis	UBERON:0004534	91.29	gold quality
left testis	UBERON:0004533	91.20	gold quality
ventricular zone	UBERON:0003053	90.72	gold quality
bronchial epithelial cell	CL:0002328	90.53	gold quality
body of pancreas	UBERON:0001150	90.19	gold quality
right atrium auricular region	UBERON:0006631	89.59	gold quality
adrenal tissue	UBERON:0018303	89.57	gold quality
testis	UBERON:0000473	89.14	gold quality
rectum	UBERON:0001052	88.36	gold quality
cardiac atrium	UBERON:0002081	88.27	gold quality
tibial nerve	UBERON:0001323	88.19	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.44	gold quality
epithelium of bronchus	UBERON:0002031	86.66	gold quality
left ovary	UBERON:0002119	86.32	gold quality
secondary oocyte	CL:0000655	86.22	gold quality
left lobe of thyroid gland	UBERON:0001120	86.21	gold quality
left adrenal gland cortex	UBERON:0035825	86.04	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	85.75	gold quality
left adrenal gland	UBERON:0001234	85.69	gold quality
bronchus	UBERON:0002185	85.66	gold quality
thyroid gland	UBERON:0002046	85.59	gold quality
right adrenal gland cortex	UBERON:0035827	85.47	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	85.36	gold quality
right lobe of thyroid gland	UBERON:0001119	85.31	gold quality
body of uterus	UBERON:0009853	85.24	gold quality
right adrenal gland	UBERON:0001233	84.97	gold quality
right ovary	UBERON:0002118	84.82	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.21

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

45 targeting CEP83, 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-4262	100.00	73.26	3931
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-181A-5P	99.99	72.96	2995
HSA-MIR-181B-5P	99.99	72.97	2996
HSA-MIR-181C-5P	99.99	72.95	2996
HSA-MIR-181D-5P	99.99	73.04	2997
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-6715A-3P	99.83	68.05	1473
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-139-5P	99.80	69.50	1399
HSA-MIR-4470	99.66	69.35	1767
HSA-MIR-545-5P	99.66	70.18	2308
HSA-MIR-378A-5P	99.65	66.33	1311
HSA-MIR-1827	99.63	68.57	3265
HSA-MIR-6513-3P	99.59	69.77	1102
HSA-MIR-7159-5P	99.53	72.12	2472
HSA-MIR-4251	99.40	69.19	3363
HSA-MIR-130A-5P	99.33	70.26	2623
HSA-MIR-3973	99.20	69.19	1990

Literature-anchored findings (GeneRIF, showing 5)

• CCDC41 is required for the docking of ciliary vesicles (PMID:23530209)
• We have identified mutations in CEP83, another distal appendages component encoding gene, as a cause of infantile nephronophthisis associated with central nervous system abnormalities in half of the individuals. (PMID:24882706)
• The results reveal a molecular mechanism of kinase regulation in ciliogenesis and identify CEP83 as a key substrate of TTBK2 during cilia initiation. (PMID:31455668)
• Beyond nephronophthisis: Retinal dystrophy in the absence of kidney dysfunction in childhood expands the clinical spectrum of CEP83 deficiency. (PMID:33938610)
• The centrosomal protein 83 (CEP83) regulates human pluripotent stem cell differentiation toward the kidney lineage. (PMID:36222666)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	cep83	ENSDARG00000101236
mus_musculus	Cep83	ENSMUSG00000020024
rattus_norvegicus	Cep83	ENSRNOG00000007859
rattus_norvegicus	AABR07039307.1	ENSRNOG00000046832

Paralogs (1): LRRC45 (ENSG00000169683)

Protein

Protein identifiers

Centrosomal protein of 83 kDa — Q9Y592 (reviewed: Q9Y592)

Alternative names: Coiled-coil domain-containing protein 41, Renal carcinoma antigen NY-REN-58

All UniProt accessions (4): Q9Y592, A0A338VFC5, F8VYN8, H0YHH5

UniProt curated annotations — full annotation on UniProt →

Function. Component of the distal appendage region of the centriole involved in the initiation of primary cilium assembly. May collaborate with IFT20 in the trafficking of ciliary membrane proteins from the Golgi complex to the cilium during the initiation of primary cilium assembly.

Subunit / interactions. Interacts with CEP164 and IFT20.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Centriole.

Disease relevance. Nephronophthisis 18 (NPHP18) [MIM:615862] An autosomal recessive disorder characterized by chronic tubulointerstitial nephritis resulting in end-stage renal disease in early childhood. Extrarenal manifestations, including intellectual disability or liver changes, may occur in some patients. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the CEP83 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9Y592-1	1	yes
Q9Y592-2	2

RefSeq proteins (13): NP_001035858, NP_001333386, NP_001333387, NP_001333388, NP_001333389, NP_001333390, NP_001333391, NP_001354966, NP_001354967, NP_001354968, NP_001354969, NP_001354970, NP_057206* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR052116	Centro_Cilium_Assembly	Family

UniProt features (19 total): sequence variant 6, sequence conflict 4, splice variant 3, coiled-coil region 2, chain 1, region of interest 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y592-F1	81.90	0.50

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): 698

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-5620912	Anchoring of the basal body to the plasma membrane
R-HSA-1852241	Organelle biogenesis and maintenance
R-HSA-5617833	Cilium Assembly

MSigDB gene sets: 183 (showing top): GOBP_PROTEIN_LOCALIZATION_TO_CYTOSKELETON, FREAC2_01, GOBP_VESICLE_MEDIATED_TRANSPORT, FOXO4_01, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_MEMBRANE_DOCKING, MODULE_205, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOBP_CILIUM_ORGANIZATION, GOCC_CENTROSOME, RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_DN, E4F1_Q6, GOBP_ORGANELLE_ASSEMBLY, CGCAAAA_MIR450

GO Biological Process (5): obsolete vesicle docking (GO:0048278), establishment of centrosome localization (GO:0051660), cilium assembly (GO:0060271), protein localization to centrosome (GO:0071539), cell projection organization (GO:0030030)

GO Molecular Function (2): identical protein binding (GO:0042802), protein binding (GO:0005515)

GO Cellular Component (7): Golgi apparatus (GO:0005794), centrosome (GO:0005813), centriole (GO:0005814), cytosol (GO:0005829), ciliary transition fiber (GO:0097539), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Assembly of the 9+0 primary cilium	1
Organelle biogenesis and maintenance	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cytoplasm	2
microtubule organizing center	2
intracellular membraneless organelle	2
cellular anatomical structure	2
centrosome localization	1
establishment of localization in cell	1
establishment of organelle localization	1
axoneme assembly	1
intraciliary transport involved in cilium assembly	1
cilium organization	1
protein localization to cilium	1
organelle assembly	1
trans-Golgi to periciliary membrane compartment transport	1
plasma membrane bounded cell projection assembly	1
ciliary transition zone assembly	1
protein localization to microtubule organizing center	1
cellular component organization	1
protein binding	1
binding	1
endomembrane system	1
intracellular membrane-bounded organelle	1
centriole	1
cilium	1
intracellular protein-containing complex	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1861 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CEP83	SCLT1	Q96NL6	994
CEP83	CEP89	Q96ST8	978
CEP83	CEP164	Q9UPV0	973
CEP83	FBF1	Q8TES7	949
CEP83	IFT20	Q8IY31	773
CEP83	ODF2	Q5BJF6	766
CEP83	TTBK2	Q6IQ55	732
CEP83	C2CD3	Q4AC94	720
CEP83	CCP110	O43303	705
CEP83	CEP97	Q8IW35	681
CEP83	CEP128	Q6ZU80	652
CEP83	IFT54	Q8TDR0	649
CEP83	TMEM67	Q5HYA8	630
CEP83	OFD1	O75665	618
CEP83	NIN	Q8N4C6	615

IntAct

24 interactions, top by confidence:

A	B	Type	Score
PSMC5	PSMD11	psi-mi:“MI:0914”(association)	0.730
HMG20A	KDM1A	psi-mi:“MI:0914”(association)	0.730
CEP83	VAPA	psi-mi:“MI:0915”(physical association)	0.400
CEP83	VAPB	psi-mi:“MI:0915”(physical association)	0.400
CEP83	H1-4	psi-mi:“MI:0915”(physical association)	0.400
CEP83	H1-5	psi-mi:“MI:0915”(physical association)	0.400
CEP83	CEP83	psi-mi:“MI:0915”(physical association)	0.370
CEP83	Tamalin	psi-mi:“MI:0915”(physical association)	0.370
MYH9	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
CEP170P1	PCYT1A	psi-mi:“MI:0914”(association)	0.350
JRKL	TIGD2	psi-mi:“MI:0914”(association)	0.350
Dctn1	DERL1	psi-mi:“MI:0914”(association)	0.350
FGFR1OP2	STK24	psi-mi:“MI:0914”(association)	0.350
PB2		psi-mi:“MI:0914”(association)	0.350
ESR1	ESYT2	psi-mi:“MI:0914”(association)	0.350
BMI1	HMGB1P1	psi-mi:“MI:0914”(association)	0.350
CEP63	CIBAR1	psi-mi:“MI:0914”(association)	0.350
REPIN1	POTEB	psi-mi:“MI:0914”(association)	0.350
CEP83	POTEB	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350
CEP83	NEDD1	psi-mi:“MI:2364”(proximity)	0.270
CEP83	ABTB3	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (56): CEP83 (Two-hybrid), NEDD1 (Proximity Label-MS), PALLD (Proximity Label-MS), SCN3A (Proximity Label-MS), SH3GLB2 (Proximity Label-MS), TP63 (Proximity Label-MS), BTBD11 (Proximity Label-MS), DVL1 (Proximity Label-MS), MIS18A (Proximity Label-MS), CEP83 (Affinity Capture-MS), CEP83 (Affinity Capture-MS), CEP83 (Affinity Capture-MS), CEP83 (Affinity Capture-MS), CEP83 (Affinity Capture-MS), CEP83 (Affinity Capture-MS)

ESM2 similar proteins: A0A8M2BID5, A0A8M9PQ61, A1Z8P9, A6QR54, B4KE73, E9Q7G0, F1R4Y7, O15083, O55156, O60437, O61308, Q11102, Q13439, Q15643, Q3SWS9, Q5DTN8, Q5M9N0, Q5PQ23, Q5RI56, Q5U4E6, Q5VZ66, Q5ZKK5, Q66H89, Q6DFL0, Q6PH08, Q6ZU80, Q7ZW57, Q811U3, Q8BI22, Q8BVL9, Q8CDI6, Q8CDI7, Q8CGB3, Q8HYY4, Q8IUD2, Q8K3M6, Q8WXW3, Q91VW5, Q96AA8, Q96N16

Diamond homologs: F1R4Y7, Q66H89, Q9D5R3, Q9Y592

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	37
Likely pathogenic	7
Uncertain significance	265
Likely benign	219
Benign	41

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1070747	NM_016122.3(CEP83):c.2007del (p.Glu669fs)	Pathogenic
1072001	NM_016122.3(CEP83):c.1060_1063del (p.Asp354fs)	Pathogenic
1072570	NM_016122.3(CEP83):c.643C>T (p.Arg215Ter)	Pathogenic
1354313	NM_016122.3(CEP83):c.1531C>T (p.Arg511Ter)	Pathogenic
139540	NM_016122.3(CEP83):c.121C>T (p.Arg41Ter)	Pathogenic
139541	NM_016122.3(CEP83):c.335_352del (p.Pro112_Leu117del)	Pathogenic
139542	NM_016122.3(CEP83):c.241C>T (p.Gln81Ter)	Pathogenic
139543	NM_016122.3(CEP83):c.2072AAC[1] (p.Gln692del)	Pathogenic
139544	NM_016122.3(CEP83):c.1532G>C (p.Arg511Pro)	Pathogenic
139546	NM_016122.3(CEP83):c.1530C>A (p.Cys510Ter)	Pathogenic
1399996	NM_016122.3(CEP83):c.1451C>A (p.Ser484Ter)	Pathogenic
1400746	NM_016122.3(CEP83):c.1867C>T (p.Gln623Ter)	Pathogenic
1427235	NM_016122.3(CEP83):c.1165C>T (p.Gln389Ter)	Pathogenic
1437595	NM_016122.3(CEP83):c.1542_1558del (p.Arg514fs)	Pathogenic
1438565	NM_016122.3(CEP83):c.1311_1315del (p.Glu437fs)	Pathogenic
1447344	NM_016122.3(CEP83):c.1621A>T (p.Lys541Ter)	Pathogenic
1453375	NM_016122.3(CEP83):c.499G>T (p.Glu167Ter)	Pathogenic
1454432	NM_016122.3(CEP83):c.1462_1465del (p.Ser488fs)	Pathogenic
1457969	NM_016122.3(CEP83):c.606del (p.Leu203fs)	Pathogenic
1935680	NM_016122.3(CEP83):c.940G>T (p.Glu314Ter)	Pathogenic
2032587	NM_016122.3(CEP83):c.1327G>T (p.Glu443Ter)	Pathogenic
2419008	NM_016122.3(CEP83):c.1948C>T (p.Gln650Ter)	Pathogenic
2426269	NC_000012.11:g.(?94794606)(94806266_?)del	Pathogenic
2707715	NM_016122.3(CEP83):c.1170del (p.Lys390fs)	Pathogenic
2721736	NM_016122.3(CEP83):c.1183C>T (p.Gln395Ter)	Pathogenic
2729193	NM_016122.3(CEP83):c.1580del (p.Thr527fs)	Pathogenic
2756615	NM_016122.3(CEP83):c.1729A>T (p.Lys577Ter)	Pathogenic
3668454	NM_016122.3(CEP83):c.1033C>T (p.Gln345Ter)	Pathogenic
3687173	NM_016122.3(CEP83):c.367C>T (p.Gln123Ter)	Pathogenic
420205	NM_016122.3(CEP83):c.1067_1068insTA (p.Glu356fs)	Pathogenic

SpliceAI

3898 predictions. Top by Δscore:

Variant	Effect	Δscore
12:94308915:CTC:C	acceptor_gain	1.0000
12:94308919:T:C	acceptor_gain	1.0000
12:94308924:A:AC	acceptor_gain	1.0000
12:94308924:A:C	acceptor_gain	1.0000
12:94308927:A:AC	acceptor_gain	1.0000
12:94308927:A:C	acceptor_gain	1.0000
12:94308929:G:GC	acceptor_gain	1.0000
12:94309912:TCATA:T	donor_loss	1.0000
12:94309913:CATAC:C	donor_loss	1.0000
12:94309914:ATACC:A	donor_loss	1.0000
12:94309915:TAC:T	donor_loss	1.0000
12:94309951:TGGA:T	donor_gain	1.0000
12:94310103:TTTGT:T	acceptor_gain	1.0000
12:94310104:TTGT:T	acceptor_gain	1.0000
12:94310105:TGT:T	acceptor_gain	1.0000
12:94310106:GT:G	acceptor_gain	1.0000
12:94310107:TC:T	acceptor_loss	1.0000
12:94310108:C:CA	acceptor_loss	1.0000
12:94310108:C:CC	acceptor_gain	1.0000
12:94310109:T:C	acceptor_gain	1.0000
12:94310109:T:TC	acceptor_gain	1.0000
12:94312909:ATTAC:A	donor_loss	1.0000
12:94313013:TTTCT:T	acceptor_gain	1.0000
12:94313014:TTCT:T	acceptor_gain	1.0000
12:94313016:CT:C	acceptor_gain	1.0000
12:94313018:C:CC	acceptor_gain	1.0000
12:94313018:CTAA:C	acceptor_loss	1.0000
12:94331845:A:C	acceptor_gain	1.0000
12:94333462:A:AC	donor_gain	1.0000
12:94333463:C:CC	donor_gain	1.0000

AlphaMissense

4639 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:94310033:A:G	F629S	0.998
12:94310032:A:C	F629L	0.997
12:94310032:A:T	F629L	0.997
12:94310034:A:G	F629L	0.997
12:94310063:A:G	L619P	0.997
12:94312957:C:G	A590P	0.997
12:94308874:A:G	L682P	0.994
12:94310044:T:A	R625S	0.994
12:94310044:T:G	R625S	0.994
12:94308865:A:G	L685P	0.993
12:94310033:A:C	F629C	0.993
12:94310030:C:G	R630P	0.992
12:94310042:T:G	H626P	0.991
12:94310075:A:G	L615P	0.991
12:94331710:G:T	A566D	0.991
12:94331720:C:G	A563P	0.990
12:94308876:T:A	R681S	0.989
12:94308876:T:G	R681S	0.989
12:94313015:T:A	R570S	0.989
12:94313015:T:G	R570S	0.989
12:94331728:A:G	L560P	0.989
12:94308886:A:G	L678P	0.988
12:94310043:G:C	H626D	0.988
12:94310024:A:G	L632P	0.987
12:94310045:C:G	R625T	0.987
12:94308841:A:G	L693P	0.984
12:94312983:A:G	L581P	0.984
12:94310046:T:C	R625G	0.983
12:94331722:C:G	R562P	0.983
12:94331717:C:G	A564P	0.982

dbSNP variants (sampled 300 via entrez): RS1000004509 (12:94293142 A>T), RS1000007225 (12:94359050 C>A,G,T), RS1000012651 (12:94458343 C>T), RS1000013022 (12:94276830 C>T), RS1000018703 (12:94408366 A>T), RS1000023258 (12:94455871 C>A,T), RS1000068777 (12:94292968 T>C), RS1000088522 (12:94385249 G>C), RS1000127345 (12:94394378 G>A,T), RS1000129783 (12:94300104 C>T), RS1000135083 (12:94449782 A>C,G,T), RS1000179822 (12:94297885 C>T), RS1000180054 (12:94276773 T>A), RS1000194924 (12:94372066 T>A,G), RS1000195588 (12:94414247 G>A)

Disease associations

OMIM: gene MIM:615847 | disease phenotypes: MIM:615862, MIM:256100

GenCC curated gene-disease

Disease	Classification	Inheritance
nephronophthisis 18	Definitive	Autosomal recessive
nephronophthisis 2	Supportive	Autosomal recessive

Mondo (5): nephronophthisis 18 (MONDO:0014374), ciliopathy (MONDO:0005308), nephronophthisis (MONDO:0019005), megacolon (MONDO:0001273), nephronophthisis 2 (MONDO:0011190)

Orphanet (3): Nephronophthisis (Orphanet:655), Microphthalmia-anophthalmia-coloboma (Orphanet:98555), Ciliopathy (Orphanet:363250)

HPO phenotypes

13 total (13 of 13 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000090	Nephronophthisis
HP:0000092	Renal tubular atrophy
HP:0000238	Hydrocephalus
HP:0000486	Strabismus
HP:0000822	Hypertension
HP:0001249	Intellectual disability
HP:0001396	Cholestasis
HP:0001970	Tubulointerstitial nephritis
HP:0003774	Stage 5 chronic kidney disease
HP:0004722	Thickened glomerular basement membrane
HP:0006580	Portal fibrosis
HP:0032118	Retinitis

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST001762_669	Obesity-related traits	9.000000e-06
GCST004278_24	Pulse pressure	2.000000e-10
GCST006030_9	Chloride levels	3.000000e-08
GCST006032_8	Sodium levels	4.000000e-08
GCST006483_8	Lung function (FVC)	3.000000e-08
GCST009391_86	Metabolite levels	8.000000e-06
GCST009798_83	Asthma	6.000000e-11
GCST012490_179	Femur bone mineral density x serum urate levels interaction	3.000000e-08
GCST012490_289	Femur bone mineral density x serum urate levels interaction	4.000000e-09

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0005763	pulse pressure measurement
EFO:0009282	sodium measurement
EFO:0004312	vital capacity
EFO:0004531	urate measurement

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
D008531	Megacolon	C06.405.469.158.701
C566582	Nephronophthisis 2 (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression	2
Tetrachlorodibenzodioxin	decreases expression	2
Valproic Acid	decreases expression, decreases methylation	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
aristolochic acid I	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	affects binding, increases activity, increases expression	1
bisphenol A	decreases methylation	1
arsenite	affects binding, decreases reaction	1
sodium arsenite	decreases expression	1
16 alpha-ethyl-21-hydroxy-19-nor-4-pregnene-3,20-dione	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
flavone	increases expression	1
epigallocatechin gallate	decreases expression, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
pentabromodiphenyl ether	increases expression	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
ICG 001	increases expression	1
abrine	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
bisphenol S	decreases methylation	1
Resveratrol	affects cotreatment, increases expression	1
Methyl Methanesulfonate	increases expression	1
Phenylmercuric Acetate	decreases expression, affects cotreatment	1
Plant Extracts	affects cotreatment, increases expression	1
Quercetin	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00068224	Not specified	COMPLETED	Clinical and Molecular Investigations Into Ciliopathies
NCT04874909	Not specified	COMPLETED	Classification, Functional Stratification and Biomarkers in Ciliopathy (CILLICORIRCM)
NCT01022957	Not specified	COMPLETED	Nephronophthisis : Clinical and Genetic Study
NCT01401998	Not specified	RECRUITING	ARPKD Database Study
NCT05286632	Not specified	COMPLETED	KidneYou - Innovative Digital Therapy
NCT06065852	Not specified	RECRUITING	National Registry of Rare Kidney Diseases
NCT06648044	Not specified	RECRUITING	Research of Therapeutic Targets in the Frame of Nephronophthisis and Renal Associated Ciliopathies
NCT04340856	Not specified	COMPLETED	Retrospective, Uncontrolled Cohort Study on the Therapy of Chronic Megalon
NCT07470892	Not specified	NOT_YET_RECRUITING	Preoperative Fish Oil PN and Prognosis After Constipation Surgery