BICC1

Summary

BICC1 (BicC family RNA binding protein 1, HGNC:19351) is a protein-coding gene on chromosome 10q21.1, encoding Protein bicaudal C homolog 1 (Q9H694). Putative RNA-binding protein.

This gene encodes an RNA-binding protein that is active in regulating gene expression by modulating protein translation during embryonic development. Mouse studies identified the corresponding protein to be under strict control during cell differentiation and to be a maternally provided gene product.

Source: NCBI Gene 80114 — RefSeq curated summary.

At a glance

• Gene–disease (curated): renal dysplasia, cystic, susceptibility to (Moderate, ClinGen)
• GWAS associations: 43
• Clinical variants (ClinVar): 454 total — 1 pathogenic, 4 likely-pathogenic
• Phenotypes (HPO): 32
• MANE Select transcript: NM_001080512

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:19351
Approved symbol	BICC1
Name	BicC family RNA binding protein 1
Location	10q21.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000122870
Ensembl biotype	protein_coding
OMIM	614295
Entrez	80114

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000263103, ENST00000373886, ENST00000476684

RefSeq mRNA: 1 — MANE Select: NM_001080512 NM_001080512

CCDS: CCDS31206

Canonical transcript exons

ENST00000373886 — 21 exons

Exon	Start	End
ENSE00000833895	58796340	58796526
ENSE00000833896	58798399	58798560
ENSE00000833897	58799056	58799252
ENSE00000833898	58800194	58800326
ENSE00000833899	58800890	58801046
ENSE00000833900	58803077	58803242
ENSE00000833901	58806584	58806623
ENSE00000833902	58807004	58807158
ENSE00001461838	58828761	58831435
ENSE00001461839	58820369	58820468
ENSE00001461841	58817562	58817722
ENSE00001461845	58813830	58813986
ENSE00001461851	58793484	58793615
ENSE00001461853	58789682	58789933
ENSE00001461855	58789262	58789456
ENSE00001461856	58788370	58788423
ENSE00001461857	58786923	58787081
ENSE00001461858	58785001	58785080
ENSE00001609109	58512872	58513333
ENSE00001642778	58620855	58620901
ENSE00001782108	58702074	58702143

Expression profiles

Bgee: expression breadth ubiquitous, 236 present calls, max score 94.48.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.1969 / max 1182.6365, expressed in 1183 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
105011	7.4017	939
105003	6.4091	970
105005	4.2717	917
105002	1.5663	786
105004	0.5481	324

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
germinal epithelium of ovary	UBERON:0001304	94.48	gold quality
renal medulla	UBERON:0000362	92.26	gold quality
parietal pleura	UBERON:0002400	92.07	gold quality
calcaneal tendon	UBERON:0003701	91.14	gold quality
metanephros cortex	UBERON:0010533	90.41	gold quality
oocyte	CL:0000023	90.31	gold quality
stromal cell of endometrium	CL:0002255	88.93	gold quality
secondary oocyte	CL:0000655	88.90	gold quality
nephron tubule	UBERON:0001231	88.69	gold quality
mucosa of paranasal sinus	UBERON:0005030	88.00	gold quality
adult mammalian kidney	UBERON:0000082	87.71	gold quality
kidney	UBERON:0002113	87.61	gold quality
pleura	UBERON:0000977	87.34	gold quality
islet of Langerhans	UBERON:0000006	86.37	gold quality
pancreas	UBERON:0001264	85.87	gold quality
periodontal ligament	UBERON:0008266	85.62	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.56	gold quality
body of pancreas	UBERON:0001150	85.56	gold quality
metanephros	UBERON:0000081	85.13	gold quality
kidney epithelium	UBERON:0004819	85.12	gold quality
tibia	UBERON:0000979	84.07	gold quality
right coronary artery	UBERON:0001625	83.68	gold quality
gall bladder	UBERON:0002110	83.34	gold quality
superficial temporal artery	UBERON:0001614	83.28	silver quality
mammary duct	UBERON:0001765	82.93	gold quality
cortex of kidney	UBERON:0001225	82.70	gold quality
caput epididymis	UBERON:0004358	82.18	gold quality
epithelium of mammary gland	UBERON:0003244	82.04	gold quality
ovary	UBERON:0000992	81.69	gold quality
skin of hip	UBERON:0001554	81.65	gold quality

Single-cell (SCXA)

Detected in 13 experiment(s), a significant marker in 13.

Experiment	Marker?	Max mean expression
E-ANND-2	yes	2799.02
E-MTAB-11268	yes	2261.68
E-GEOD-70580	yes	321.75
E-GEOD-135922	yes	48.69
E-CURD-119	yes	35.97
E-ANND-3	yes	34.66
E-MTAB-5061	yes	27.56
E-MTAB-10553	yes	23.81
E-GEOD-81547	yes	21.65
E-GEOD-83139	yes	12.92
E-HCAD-9	yes	8.76
E-ENAD-27	yes	6.85
E-HCAD-35	yes	6.51

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 14)

• The nonsense mutation identified in BICC1 and associated with cystic renal dysplasia results in a complete loss of Wnt inhibitory activity. The point mutation in the SAM domain results in a 22% loss of activity. (PMID:21922595)
• The minor T-allele of BICC1 has a protective role against major depressive disorder and its known structural and functional brain changes. (PMID:22910460)
• Polymorphisms in intron 2 of BICC1 are associated with its expression and bone mineral density (BMD) (PMID:24789909)
• identify Bicc1 as a genetic determinant of osteoblastogenesis and BMD and suggest that it does so by regulating Pkd2 transcript levels (PMID:24789909)
• findings identify a role for increased levels of BICC1 in the pathophysiology of depressive behavior (PMID:25178406)
• Results provide some support for the involvement of BICC1 and PCLO in late-life depressive disorders and preliminary evidence that these genetic variants may also influence brain structural volumes (PMID:26391493)
• Suggest allelic changes in the regulation of the BICC1 gene in amygdala neurones may contribute to mood disorders. (PMID:26440730)
• Our findings suggested rs17648524 (intronic RBFOX1 gene) and rs7084402 (7.5kb 5’ of the BICC1 gene) showed gender-specific associations with high myopia in the Han Chinese. (PMID:28085524)
• The authors demonstrate that OFD1 cooperates with the mRNA binding protein Bicc1 to functionally control the protein synthesis machinery at the centrosome where also the PIC and eIF4F components were shown to localize in mammalian cells. (PMID:28450740)
• genetic variants in BICC1 and RASGRF1 are closely associated with high myopia, which appears to be a potential candidate for high myopia in Chinese Han population. (PMID:29044055)
• Data identified a significantly differentially methylated cg09696939 near gene BICC1 to be associated with cleft lip and cleft palate. (PMID:30832715)
• miR-101-3p and miR-199b-5p promote cell apoptosis in oral cancer by targeting BICC1. (PMID:32259627)
• BICC1 as a novel prognostic biomarker in gastric cancer correlating with immune infiltrates. (PMID:32736193)
• Lymph node metastasis related gene BICC1 promotes tumor progression by promoting EMT and immune infiltration in pancreatic cancer. (PMID:37880742)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	bicc1a	ENSDARG00000061682
danio_rerio	bicc1b	ENSDARG00000070497
mus_musculus	Bicc1	ENSMUSG00000014329
rattus_norvegicus	Bicc1	ENSRNOG00000000614

Paralogs (2): HDLBP (ENSG00000115677), ANKS6 (ENSG00000165138)

Protein

Protein identifiers

Protein bicaudal C homolog 1 — Q9H694 (reviewed: Q9H694)

All UniProt accessions (2): A6NGY7, Q9H694

UniProt curated annotations — full annotation on UniProt →

Function. Putative RNA-binding protein. Acts as a negative regulator of Wnt signaling. May be involved in regulating gene expression during embryonic development.

Subunit / interactions. Interacts (via KH domains) with ANKS6 (via SAM domain) in an RNA-dependent manner. Interacts with ANKS3.

Subcellular location. Cytoplasm.

Disease relevance. Renal dysplasia, cystic (CYSRD) [MIM:601331] An anomaly of the kidney characterized by numerous renal cysts and apparent disorder of differentiation of the renal parenchyma. Kidney of affected individuals lack the normal renal bean shape, and the collection drainage system. The cystic, dysplastic kidney contains undifferentiated mesenchyme, cartilaginous tissue, and immature collecting ducts. Disease susceptibility is associated with variants affecting the gene represented in this entry.

Similarity. Belongs to the BicC family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9H694-1	1	yes
Q9H694-2	2

RefSeq proteins (1): NP_001073981* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001660	SAM	Domain
IPR004087	KH_dom	Domain
IPR004088	KH_dom_type_1	Domain
IPR013761	SAM/pointed_sf	Homologous_superfamily
IPR036612	KH_dom_type_1_sf	Homologous_superfamily
IPR037974	BICC1_SAM_dom	Domain
IPR047549	BICC1_KH-I_rpt1	Domain
IPR047553	BICC1_KH-I_rpt3	Domain
IPR047554	BICC1_KH-I_rpt2	Domain
IPR054727	BICC1_KH	Domain

Pfam: PF00013, PF00536, PF22985, PF24234

UniProt features (38 total): helix 11, modified residue 7, sequence variant 6, region of interest 4, domain 3, strand 3, compositionally biased region 2, chain 1, splice variant 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
4RQM	X-RAY DIFFRACTION	1.75
6GY4	X-RAY DIFFRACTION	1.99
4RQN	X-RAY DIFFRACTION	2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H694-F1	61.02	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 (7): 26, 31, 43, 398, 576, 612, 679

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 262 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_DN, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_MACROMOLECULE_CATABOLIC_PROCESS, chr10q21, GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, GOBP_SPECIFICATION_OF_SYMMETRY, MARTINEZ_RB1_TARGETS_DN, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1, GOBP_CANONICAL_WNT_SIGNALING_PATHWAY, RIGGI_EWING_SARCOMA_PROGENITOR_DN, ONDER_CDH1_TARGETS_2_UP, CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN, PPARA_01, GOBP_NEGATIVE_REGULATION_OF_WNT_SIGNALING_PATHWAY, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM

GO Biological Process (5): kidney development (GO:0001822), mRNA catabolic process (GO:0006402), determination of left/right symmetry (GO:0007368), heart development (GO:0007507), negative regulation of canonical Wnt signaling pathway (GO:0090090)

GO Molecular Function (3): RNA binding (GO:0003723), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
animal organ development	2
binding	2
renal system development	1
RNA catabolic process	1
negative regulation of gene expression	1
mRNA metabolic process	1
determination of bilateral symmetry	1
left/right pattern formation	1
circulatory system development	1
negative regulation of Wnt signaling pathway	1
canonical Wnt signaling pathway	1
regulation of canonical Wnt signaling pathway	1
nucleic acid binding	1
intracellular anatomical structure	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1214 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
BICC1	PPHLN1	Q8NEY8	739
BICC1	ANKS3	Q6ZW76	691
BICC1	FGFR2	P18443	679
BICC1	AHCYL1	O43865	661
BICC1	TACC3	Q9Y6A5	653
BICC1	ANKS6	Q68DC2	648
BICC1	FGFR1	P11362	597
BICC1	NEK8	Q86SG6	592
BICC1	SHTN1	A0MZ66	588
BICC1	NEK9	Q8TD19	562
BICC1	BAIAP2L1	Q9UHR4	519
BICC1	AFF3	P51826	507
BICC1	TACC1	O75410	481
BICC1	RET	P07949	480
BICC1	CNOT3	O75175	455

IntAct

16 interactions, top by confidence:

A	B	Type	Score
YWHAG	BLTP3B	psi-mi:“MI:0914”(association)	0.640
YWHAH	BLTP3B	psi-mi:“MI:0914”(association)	0.570
YWHAB	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
YWHAQ	PLEKHG3	psi-mi:“MI:0914”(association)	0.480
GABARAP	BICC1	psi-mi:“MI:0407”(direct interaction)	0.440
GABARAPL2	BICC1	psi-mi:“MI:0407”(direct interaction)	0.440
Cep152	SH3PXD2B	psi-mi:“MI:0914”(association)	0.350
TFG	NCOA4	psi-mi:“MI:0914”(association)	0.350
CAPZA2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
BVLF1	VWA8	psi-mi:“MI:0914”(association)	0.350
NEK7	SUPT5H	psi-mi:“MI:0914”(association)	0.350
YWHAQ	MCRIP1	psi-mi:“MI:0914”(association)	0.350
ANKS3	TNKS	psi-mi:“MI:0914”(association)	0.350
KLHL22	TRAV18	psi-mi:“MI:0914”(association)	0.350
CREB3L2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350

BioGRID (35): BICC1 (Affinity Capture-MS), BICC1 (Affinity Capture-MS), BICC1 (Affinity Capture-MS), BICC1 (Affinity Capture-RNA), BICC1 (Synthetic Lethality), BICC1 (Affinity Capture-MS), BICC1 (Proximity Label-MS), BICC1 (Proximity Label-MS), BICC1 (Proximity Label-MS), BICC1 (Proximity Label-MS), BICC1 (Proximity Label-MS), BICC1 (Proximity Label-MS), BICC1 (Proximity Label-MS), BICC1 (Proximity Label-MS), BICC1 (Proximity Label-MS)

ESM2 similar proteins: A0A0B4KGY6, A8MPH9, B4JYN3, B4K617, B4KXJ5, B4M5T7, B4MLR8, G5EFF1, G5EFL9, M9PH32, O01367, P12349, P17970, P21525, P34021, P34611, P49880, P51023, Q01295, Q01617, Q03297, Q24167, Q24767, Q29AP1, Q2LZ59, Q56R14, Q5U4T7, Q6E2N3, Q6YGZ4, Q7KVW5, Q7YU81, Q8IPW2, Q8IQG1, Q8IXF0, Q8MQJ9, Q8QGQ6, Q8T498, Q960C5, Q99MQ1, Q9BJZ5

Diamond homologs: A4II29, E9Q238, F1MJR8, O83515, P0C0T2, Q01317, Q05823, Q05921, Q14678, Q1LZH7, Q21920, Q24009, Q5M9H0, Q5SUE8, Q5U4T7, Q5U5A6, Q5XJ13, Q68DC2, Q6AI12, Q6GQX6, Q6NY19, Q6ZW76, Q7T3X9, Q7T3Y0, Q7Z6K4, Q8BX02, Q8IWB6, Q91ZA8, Q99MQ1, Q9CZK6, Q9H694, Q9IA00, Q9Z1P7, Q54HW1, Q9XZC0, Q8N8V4, O08764, Q3KP44, Q502M6, Q63ZY3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 23 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Transcriptional Regulation by TP53	5	18.2×	6e-05
Membrane Trafficking	6	13.1×	5e-05
Vesicle-mediated transport	6	12.3×	6e-05
Cell Cycle	5	10.6×	5e-04
Signaling by Rho GTPases	5	10.1×	6e-04
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	5	9.8×	6e-04
Viral Infection Pathways	5	9.1×	9e-04
Infectious disease	5	7.3×	2e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	4
Uncertain significance	261
Likely benign	120
Benign	37

Top pathogenic / likely-pathogenic (5)

Variant ID	HGVS	Classification
1048654	NM_001080512.3(BICC1):c.93del (p.Glu32fs)	Pathogenic
1328431	NM_001080512.3(BICC1):c.387+1G>C	Likely pathogenic
3066390	NM_001080512.3(BICC1):c.2229_2230insGA (p.Lys744fs)	Likely pathogenic
3234043	NM_001080512.3(BICC1):c.1827del (p.Glu609fs)	Likely pathogenic
3236040	NM_001080512.3(BICC1):c.1179+1G>T	Likely pathogenic

SpliceAI

5594 predictions. Top by Δscore:

Variant	Effect	Δscore
10:58513308:G:GT	donor_gain	1.0000
10:58513330:CAAGG:C	donor_loss	1.0000
10:58513332:AGG:A	donor_loss	1.0000
10:58513334:GTA:G	donor_loss	1.0000
10:58620853:A:AG	acceptor_gain	1.0000
10:58620854:G:GG	acceptor_gain	1.0000
10:58620854:GCT:G	acceptor_gain	1.0000
10:58702060:A:AG	acceptor_gain	1.0000
10:58702066:T:TA	acceptor_gain	1.0000
10:58702069:TACAG:T	acceptor_loss	1.0000
10:58702071:CAGAT:C	acceptor_loss	1.0000
10:58702072:A:AC	acceptor_loss	1.0000
10:58702072:A:AG	acceptor_gain	1.0000
10:58702073:G:GA	acceptor_gain	1.0000
10:58702073:GA:G	acceptor_gain	1.0000
10:58702073:GAT:G	acceptor_gain	1.0000
10:58702073:GATC:G	acceptor_gain	1.0000
10:58702073:GATCA:G	acceptor_gain	1.0000
10:58702139:GAAAG:G	donor_gain	1.0000
10:58702140:AAAG:A	donor_loss	1.0000
10:58702142:AGGTA:A	donor_loss	1.0000
10:58702143:GGTAA:G	donor_loss	1.0000
10:58702144:G:A	donor_loss	1.0000
10:58702145:T:G	donor_loss	1.0000
10:58725784:G:GT	donor_gain	1.0000
10:58725830:G:T	donor_gain	1.0000
10:58784998:TA:T	acceptor_loss	1.0000
10:58784999:A:AG	acceptor_gain	1.0000
10:58785000:G:GG	acceptor_gain	1.0000
10:58785000:GA:G	acceptor_gain	1.0000

AlphaMissense

6384 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:58513291:C:A	R50S	1.000
10:58513291:C:T	R50C	1.000
10:58513294:T:C	F51L	1.000
10:58513295:T:C	F51S	1.000
10:58513295:T:G	F51C	1.000
10:58513296:C:A	F51L	1.000
10:58513296:C:G	F51L	1.000
10:58513297:C:A	R52S	1.000
10:58513300:G:A	V53M	1.000
10:58513301:T:A	V53E	1.000
10:58513303:G:C	D54H	1.000
10:58513304:A:T	D54V	1.000
10:58513306:A:G	R55G	1.000
10:58513306:A:T	R55W	1.000
10:58513307:G:C	R55T	1.000
10:58513307:G:T	R55M	1.000
10:58513308:G:C	R55S	1.000
10:58513308:G:T	R55S	1.000
10:58513316:T:A	L58H	1.000
10:58513316:T:C	L58P	1.000
10:58513318:G:A	E59K	1.000
10:58513320:G:C	E59D	1.000
10:58513320:G:T	E59D	1.000
10:58513328:T:C	L62S	1.000
10:58620891:T:C	F76S	1.000
10:58620893:T:C	F77L	1.000
10:58620894:T:C	F77S	1.000
10:58620895:T:A	F77L	1.000
10:58620895:T:G	F77L	1.000
10:58702099:T:A	I88N	1.000

dbSNP variants (sampled 300 via entrez): RS1000024840 (10:58630762 G>A), RS1000025774 (10:58685035 C>A,T), RS1000026657 (10:58590083 G>T), RS1000062069 (10:58769634 A>G,T), RS1000063542 (10:58572149 T>C), RS1000069499 (10:58582418 C>T), RS1000098425 (10:58666340 A>C,G), RS1000103618 (10:58751378 C>A), RS1000116076 (10:58695838 A>G), RS1000117860 (10:58703001 A>C), RS1000122082 (10:58756846 A>C), RS1000124335 (10:58782682 A>C,G,T), RS1000126376 (10:58554844 G>A), RS1000129027 (10:58531669 A>G), RS1000145082 (10:58706225 C>A,G,T)

Disease associations

OMIM: gene MIM:614295 | disease phenotypes: MIM:601331, MIM:191830, MIM:610805

GenCC curated gene-disease

Disease	Classification	Inheritance
renal dysplasia, cystic, susceptibility to	Moderate	Autosomal dominant

ClinGen Gene-Disease Validity (1)

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

Disease	Classification	Inheritance
renal dysplasia, cystic, susceptibility to	Moderate	AD

Mondo (3): renal dysplasia, cystic, susceptibility to (MONDO:0011037), renal agenesis (MONDO:0018470), congenital anomaly of kidney and urinary tract (MONDO:0019719)

Orphanet (2): Renal agenesis (Orphanet:411709), Renal or urinary tract malformation (Orphanet:93545)

HPO phenotypes

32 total (30 of 32 shown, HPO-id order):

HPO	Term
HP:0000006	Autosomal dominant inheritance
HP:0000010	Recurrent urinary tract infections
HP:0000076	Vesicoureteral reflux
HP:0000083	Renal insufficiency
HP:0000105	Enlarged kidney
HP:0000107	Renal cyst
HP:0000110	Renal dysplasia
HP:0000790	Hematuria
HP:0000791	Uric acid nephrolithiasis
HP:0000800	Cystic renal dysplasia
HP:0000822	Hypertension
HP:0001407	Hepatic cysts
HP:0001634	Mitral valve prolapse
HP:0001737	Pancreatic cysts
HP:0002616	Aortic root aneurysm
HP:0003259	Elevated circulating creatinine concentration
HP:0003774	Stage 5 chronic kidney disease
HP:0004719	Hyperechogenic kidneys
HP:0004944	Dilatation of the cerebral artery
HP:0006557	Polycystic liver disease
HP:0008672	Calcium oxalate nephrolithiasis
HP:0011004	Abnormal systemic arterial morphology
HP:0011760	Pituitary growth hormone cell adenoma
HP:0012207	Reduced sperm motility
HP:0012213	Decreased glomerular filtration rate
HP:0012330	Pyelonephritis
HP:0012591	Abnormal urinary electrolyte concentration
HP:0012592	Albuminuria
HP:0012622	Chronic kidney disease
HP:0030157	Flank pain

GWAS associations

43 associations (top):

Study	Trait	p-value
GCST001762_59	Obesity-related traits	7.000000e-06
GCST001858_2	Refractive error	2.000000e-13
GCST002932_16	Manganese levels	8.000000e-06
GCST003455_17	Spherical equivalent (joint analysis main effects and education interaction)	3.000000e-07
GCST003455_40	Spherical equivalent (joint analysis main effects and education interaction)	3.000000e-09
GCST003542_26	Night sleep phenotypes	3.000000e-06
GCST003997_4	Myopia	3.000000e-14
GCST004283_11	Midgestational circulating levels of PCBs	2.000000e-06
GCST004764_5	LDL cholesterol change in response to fenofibrate in statin-treated type 2 diabetes	4.000000e-07
GCST004765_5	Total cholesterol change in response to fenofibrate in statin-treated type 2 diabetes	8.000000e-11
GCST005024_8	Pursuit maintenance gain	1.000000e-06
GCST005983_34	Serum uric acid levels	4.000000e-17
GCST005986_14	Blood urea nitrogen levels	2.000000e-09
GCST005995_2	Hemoglobin	4.000000e-08
GCST006065_39	Glaucoma (primary open-angle)	7.000000e-09
GCST006291_139	Spherical equivalent or myopia (age of diagnosis)	4.000000e-21
GCST006395_28	Glaucoma	9.000000e-09
GCST006979_584	Heel bone mineral density	5.000000e-25
GCST006979_585	Heel bone mineral density	6.000000e-09
GCST007096_104	Pulse pressure	5.000000e-09
GCST007565_65	Morning person	7.000000e-17
GCST007576_354	Chronotype	7.000000e-17
GCST007725_3	Serum uric acid levels	2.000000e-18
GCST007733_70	Serum uric acid levels	2.000000e-06
GCST007930_21	Medication use (agents acting on the renin-angiotensin system)	2.000000e-08
GCST008062_81	Blood urea nitrogen levels	1.000000e-12
GCST008971_53	Urate levels	4.000000e-19
GCST008972_103	Urate levels	5.000000e-20
GCST008972_188	Urate levels	3.000000e-39
GCST009722_5	Glaucoma (multi-trait analysis)	1.000000e-13

EFO canonical traits (19, from GWAS)

EFO ID	Trait name
EFO:0004784	self reported educational attainment
EFO:0007827	nighttime rest measurement
EFO:0007042	polychlorinated biphenyls measurement
EFO:0007964	gestational serum measurement
EFO:0007804	LDL cholesterol change measurement
EFO:0007806	total cholesterol change measurement
EFO:0008433	pursuit maintenance gain measurement
EFO:0004761	uric acid measurement
EFO:0004509	hemoglobin measurement
EFO:0004847	age at onset
EFO:0009270	heel bone mineral density
EFO:0005763	pulse pressure measurement
EFO:0008328	chronotype measurement
EFO:0009931	Agents acting on the renin-angiotensin system use measurement
EFO:0004531	urate measurement
EFO:0004695	intraocular pressure measurement
EFO:0004348	hematocrit
EFO:0004532	serum gamma-glutamyl transferase measurement
EFO:0007788	BMI-adjusted waist-hip ratio

MeSH disease descriptors (2)

Descriptor	Name	Tree numbers
C566906	Cakut (supp.)
C537755	Renal dysplasia diffuse cystic (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, decreases expression, decreases methylation	6
sodium arsenite	increases abundance, decreases expression	3
Air Pollutants	decreases expression, increases abundance, increases expression	3
Tetrachlorodibenzodioxin	increases expression	3
Aflatoxin B1	affects expression, decreases methylation, increases methylation	3
Particulate Matter	decreases expression, increases abundance, affects cotreatment	3
Benzo(a)pyrene	increases methylation, decreases expression, decreases methylation	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Tobacco Smoke Pollution	decreases expression, increases expression	2
Cyclosporine	decreases expression, increases methylation	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
pirinixic acid	affects binding, increases activity, increases expression	1
bisphenol A	increases expression	1
glycidyl methacrylate	increases expression	1
beta-lapachone	decreases expression	1
arsenite	affects binding, decreases reaction	1
mono-(2-ethylhexyl)phthalate	decreases expression	1
butyraldehyde	decreases expression	1
nickel sulfate	decreases expression	1
3-nitrobenzanthrone	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	increases expression, affects cotreatment	1
dorsomorphin	increases expression, affects cotreatment	1
eprenetapopt	affects expression, affects reaction	1
bisphenol S	increases methylation	1
jinfukang	affects cotreatment, decreases expression	1
Leflunomide	increases expression	1
Ethanol	affects cotreatment, decreases expression, increases abundance	1
Arsenic	decreases expression, increases abundance	1
Cisplatin	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT04115345	PHASE1	COMPLETED	A Study of a Renal Autologous Cell Therapy (REACT) in Patients With Chronic Kidney Disease (CKD) From Congenital Anomalies of the Kidney and Urinary Tract (CAKUT).
NCT05694169	PHASE1	TERMINATED	A Study of Participants With Chronic Kidney Disease Previously Treated With REACT
NCT04537364	Not specified	COMPLETED	Prediction of Renal Parenchymal Damage of CAKUT
NCT06921733	Not specified	RECRUITING	Ultrasound Localization Microscopy in Patient With Congenital Anomalies of the Kidney and Urinary Tract (CAKUT)