WNT9B

Summary

WNT9B (Wnt family member 9B, HGNC:12779) is a protein-coding gene on chromosome 17q21.32, encoding Protein Wnt-9b (O14905). Ligand for members of the frizzled family of seven transmembrane receptors.

The WNT gene family consists of structurally related genes that encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family. Study of its expression in the teratocarcinoma cell line NT2 suggests that it may be implicated in the early process of neuronal differentiation of NT2 cells induced by retinoic acid. This gene is clustered with WNT3, another family member, in the chromosome 17q21 region. Alternative splicing results in multiple transcript variants.

Source: NCBI Gene 7484 — RefSeq curated summary.

At a glance

• Gene–disease (curated): renal agenesis (Moderate, GenCC)
• GWAS associations: 6
• Clinical variants (ClinVar): 8 total
• Phenotypes (HPO): 18
• MANE Select transcript: NM_003396

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:12779
Approved symbol	WNT9B
Name	Wnt family member 9B
Location	17q21.32
Locus type	gene with protein product
Status	Approved
Aliases	WNT14B
Ensembl gene	ENSG00000158955
Ensembl biotype	protein_coding
OMIM	602864
Entrez	7484

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000290015, ENST00000393461, ENST00000575372

RefSeq mRNA: 2 — MANE Select: NM_003396 NM_001320458, NM_003396

CCDS: CCDS11506, CCDS82147

Canonical transcript exons

ENST00000290015 — 4 exons

Exon	Start	End
ENSE00001042251	46876245	46880560
ENSE00001042252	46875101	46875366
ENSE00001173104	46872517	46872773
ENSE00003843157	46851583	46851715

Expression profiles

Bgee: expression breadth ubiquitous, 114 present calls, max score 71.73.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.3112 / max 35.8805, expressed in 127 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
161328	0.3112	127

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
quadriceps femoris	UBERON:0001377	71.73	gold quality
metanephros cortex	UBERON:0010533	70.81	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	67.44	gold quality
thymus	UBERON:0002370	66.88	silver quality
cerebellar vermis	UBERON:0004720	66.15	gold quality
duodenum	UBERON:0002114	66.14	gold quality
adult mammalian kidney	UBERON:0000082	63.34	gold quality
kidney	UBERON:0002113	62.93	gold quality
prefrontal cortex	UBERON:0000451	60.14	gold quality
placenta	UBERON:0001987	59.73	gold quality
apex of heart	UBERON:0002098	59.34	gold quality
frontal cortex	UBERON:0001870	59.09	gold quality
superior frontal gyrus	UBERON:0002661	58.93	gold quality
primary visual cortex	UBERON:0002436	58.62	gold quality
right frontal lobe	UBERON:0002810	57.74	gold quality
right atrium auricular region	UBERON:0006631	57.26	gold quality
cortex of kidney	UBERON:0001225	56.81	gold quality
skin of abdomen	UBERON:0001416	56.74	gold quality
cerebral cortex	UBERON:0000956	56.69	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	56.64	gold quality
spleen	UBERON:0002106	56.48	gold quality
heart left ventricle	UBERON:0002084	56.18	gold quality
heart	UBERON:0000948	55.81	gold quality
anterior cingulate cortex	UBERON:0009835	55.64	gold quality
Brodmann (1909) area 9	UBERON:0013540	55.64	gold quality
mucosa of stomach	UBERON:0001199	54.85	gold quality
right hemisphere of cerebellum	UBERON:0014890	54.48	gold quality
zone of skin	UBERON:0000014	53.12	gold quality
Ammon’s horn	UBERON:0001954	52.73	gold quality
cerebellum	UBERON:0002037	52.61	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.32

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

235 targeting WNT9B, 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-3120-5P	100.00	65.56	965
HSA-MIR-5193	100.00	67.26	1744
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-4500	99.99	72.72	2367
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-302E	99.96	70.74	2669
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-9-3P	99.96	70.88	2068

Literature-anchored findings (GeneRIF, showing 14)

• Mutations in the coding sequence of WNT4, WNT5A, WNT7A, and WNT9B are not responsible for the Mayer-Rokitansky-Kuster-Hauser syndrome. (PMID:19171330)
• secretion of WNT2B and WNT9B and stabilization of beta-catenin (CTNNB1) upon virus infection negatively regulate expression of representative inducible genes IFNB1, IFIT1 and TNF in a CTNNB1-dependent effector mechanism (PMID:23785285)
• The signals from the stromal fibroblasts cooperate with Wnt9b to promote differentiation of the progenitor cells. (PMID:23974041)
• Two novel mutations (a missense mutation in exon 1, and one in the 3-UTR) may be pathogenic variants in Mayer-Rokitansky-Kuster-Hauser syndrome patients and warrant further functional study. (PMID:24268733)
• Our study further supports the involvement of WNT9B as a cleft susceptibility gene in Brazilian families experiencing NSCL+/-P. Although additional studies are still necessary to unveil the exact mechanism by which WNT genes would contribute to NSCL+/-P, allelic polymorphisms in these genes and their interactions may partly explain the variance of individual susceptibility to NSCL+/-P. (PMID:24437584)
• results indicate that mutations in the coding sequence of WNT9B are not responsible for Mullerian duct abnormalities in the Chinese population (PMID:24581601)
• Genome association study shows a highly conserved 32 kb intergenic region containing regulatory elements between WNT3 and WNT9B in patients with classic bladder exstrophy. (PMID:24852367)
• This association study successfully identified two susceptibility Single Nucleotide Polymorphisms, (WNT9B and PBX1) associated with Mayer-Rokitansky-Kuster-Hauser syndrome risk, both separately and interactively. (PMID:26075712)
• Multi-layered mutation in hedgehog-related genes in Gorlin syndrome may affect the phenotype (PMID:28915250)
• Circulating Exosomal miR-20b-5p Inhibition Restores Wnt9b Signaling and Reverses Diabetes-Associated Impaired Wound Healing. (PMID:31867895)
• Canonical Wnts Mediate CD8(+) T Cell Noncytolytic Anti-HIV-1 Activity and Correlate with HIV-1 Clinical Status. (PMID:32887752)
• Genetic Variation in WNT9B Increases Relapse Hazard in Multiple Sclerosis. (PMID:33704824)
• Homozygous WNT9B variants in two families with bilateral renal agenesis/hypoplasia/dysplasia. (PMID:34145744)
• Wnt Family Member 9b (Wnt9b) Is a New Sensitive and Specific Marker for Breast Cancer. (PMID:34324458)

Cross-species orthologs

9 orthologs

Organism	Symbol	Gene ID
danio_rerio	wnt9b	ENSDARG00000037889
mus_musculus	Wnt9b	ENSMUSG00000018486
rattus_norvegicus	Wnt9b	ENSRNOG00000003807
drosophila_melanogaster	Wnt2	FBGN0004360
drosophila_melanogaster	Wnt5	FBGN0010194
drosophila_melanogaster	Wnt10	FBGN0031903
caenorhabditis_elegans		WBGENE00000857
caenorhabditis_elegans		WBGENE00000858
caenorhabditis_elegans	lin-44	WBGENE00003029

Paralogs (18): WNT16 (ENSG00000002745), WNT8A (ENSG00000061492), WNT8B (ENSG00000075290), WNT11 (ENSG00000085741), WNT2 (ENSG00000105989), WNT3 (ENSG00000108379), WNT5B (ENSG00000111186), WNT5A (ENSG00000114251), WNT6 (ENSG00000115596), WNT1 (ENSG00000125084), WNT2B (ENSG00000134245), WNT10A (ENSG00000135925), WNT9A (ENSG00000143816), WNT3A (ENSG00000154342), WNT7A (ENSG00000154764), WNT4 (ENSG00000162552), WNT10B (ENSG00000169884), WNT7B (ENSG00000188064)

Protein

Protein identifiers

Protein Wnt-9b — O14905 (reviewed: O14905)

Alternative names: Protein Wnt-14b, Protein Wnt-15

All UniProt accessions (3): O14905, E7EPC3, I3L0L8

UniProt curated annotations — full annotation on UniProt →

Function. Ligand for members of the frizzled family of seven transmembrane receptors. Functions in the canonical Wnt/beta-catenin signaling pathway. Required for normal embryonic kidney development, and for normal development of the urogenital tract, including uterus and part of the oviduct and the upper vagina in females, and epididymis and vas deferens in males. Activates a signaling cascade in the metanephric mesenchyme that induces tubulogenesis. Acts upstream of WNT4 in the signaling pathways that mediate development of kidney tubules and the Muellerian ducts. Plays a role in cranofacial development and is required for normal fusion of the palate during embryonic development.

Subunit / interactions. Forms a soluble 1:1 complex with AFM; this prevents oligomerization and is required for prolonged biological activity. The complex with AFM may represent the physiological form in body fluids. Component of the Wnt-Fzd-LRP5-LRP6 signaling complex that contains a WNT protein, a FZD protein and LRP5 or LRP6. Interacts directly in the complex with LRP6. Interacts with PKD1 (via extracellular domain).

Subcellular location. Secreted. Extracellular space. Extracellular matrix.

Tissue specificity. Moderately expressed in fetal kidney and adult kidney. Also found in brain.

Post-translational modifications. Palmitoleoylation is required for efficient binding to frizzled receptors. Depalmitoleoylation leads to Wnt signaling pathway inhibition.

Similarity. Belongs to the Wnt family.

RefSeq proteins (2): NP_001307387, NP_003387* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR005817	Wnt	Family
IPR018161	Wnt_CS	Conserved_site
IPR043158	Wnt_C	Homologous_superfamily

Pfam: PF00110

UniProt features (16 total): disulfide bond 11, signal peptide 1, chain 1, sequence variant 1, lipid moiety-binding region 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O14905-F1	84.50	0.60

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): 216

Disulfide bonds (11): 305–311, 315–355, 331–346, 333–343, 338–339, 89–100, 135–143, 145–162, 210–224, 212–219, 291–316

Glycosylation sites (1): 99

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-3238698	WNT ligand biogenesis and trafficking
R-HSA-373080	Class B/2 (Secretin family receptors)
R-HSA-9831926	Nephron development

MSigDB gene sets: 299 (showing top): GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, GOBP_METANEPHRIC_NEPHRON_MORPHOGENESIS, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_EPITHELIUM_DEVELOPMENT, GOBP_SOMATIC_STEM_CELL_POPULATION_MAINTENANCE, GOBP_METANEPHROS_DEVELOPMENT, KEGG_HEDGEHOG_SIGNALING_PATHWAY, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_CELLULAR_RESPONSE_TO_LIPID, GOBP_MESENCHYMAL_TO_EPITHELIAL_TRANSITION, GOBP_METANEPHRIC_EPITHELIUM_DEVELOPMENT, GOBP_MALE_GENITALIA_DEVELOPMENT, GOBP_EMBRYONIC_SKELETAL_SYSTEM_DEVELOPMENT, CMYB_01, GOBP_NON_CANONICAL_WNT_SIGNALING_PATHWAY

GO Biological Process (34): branching involved in ureteric bud morphogenesis (GO:0001658), in utero embryonic development (GO:0001701), regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003339), cellular response to starvation (GO:0009267), regulation of asymmetric cell division (GO:0009786), neuron differentiation (GO:0030182), male genitalia development (GO:0030539), response to retinoic acid (GO:0032526), regulation of tube size (GO:0035150), non-canonical Wnt signaling pathway (GO:0035567), cell fate commitment (GO:0045165), embryonic cranial skeleton morphogenesis (GO:0048701), roof of mouth development (GO:0060021), canonical Wnt signaling pathway (GO:0060070), Wnt signaling pathway, planar cell polarity pathway (GO:0060071), uterus morphogenesis (GO:0061038), cornea development in camera-type eye (GO:0061303), cellular response to retinoic acid (GO:0071300), kidney rudiment formation (GO:0072003), mesenchymal stem cell maintenance involved in nephron morphogenesis (GO:0072038), collecting duct development (GO:0072044), establishment of planar polarity involved in nephron morphogenesis (GO:0072046), metanephric tubule formation (GO:0072174), mesonephric duct formation (GO:0072181), negative regulation of stem cell population maintenance (GO:1902455), midbrain dopaminergic neuron differentiation (GO:1904948), kidney development (GO:0001822), multicellular organism development (GO:0007275), Wnt signaling pathway (GO:0016055), branching morphogenesis of an epithelial tube (GO:0048754), kidney morphogenesis (GO:0060993), nephron tubule morphogenesis (GO:0072078), mesonephric tubule development (GO:0072164), metanephric tubule development (GO:0072170)

GO Molecular Function (5): frizzled binding (GO:0005109), cytokine activity (GO:0005125), co-receptor binding (GO:0039706), receptor ligand activity (GO:0048018), signaling receptor binding (GO:0005102)

GO Cellular Component (2): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Signaling by WNT	1
GPCR ligand binding	1
Kidney development	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell differentiation	2
Wnt signaling pathway	2
anatomical structure development	2
protein binding	2
branching morphogenesis of an epithelial tube	1
ureteric bud morphogenesis	1
chordate embryonic development	1
mesenchymal to epithelial transition involved in metanephros morphogenesis	1
regulation of epithelial cell differentiation involved in kidney development	1
cellular response to nutrient levels	1
cellular response to stress	1
response to starvation	1
asymmetric cell division	1
regulation of cell division	1
generation of neurons	1
male sex differentiation	1
genitalia development	1
reproductive system development	1
response to lipid	1
response to oxygen-containing compound	1
regulation of anatomical structure size	1
cellular developmental process	1
embryonic skeletal system morphogenesis	1
cranial skeletal system development	1
non-canonical Wnt signaling pathway	1
developmental process involved in reproduction	1
animal organ morphogenesis	1
uterus development	1
camera-type eye development	1
response to retinoic acid	1
cellular response to lipid	1
cellular response to oxygen-containing compound	1
anatomical structure formation involved in morphogenesis	1
kidney morphogenesis	1
somatic stem cell population maintenance	1
nephron morphogenesis	1
G protein-coupled receptor binding	1
receptor ligand activity	1
signaling receptor binding	1
signal transduction	1

Protein interactions and networks

STRING

1158 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
WNT9B	SIX2	Q9NPC8	712
WNT9B	LRP6	O75581	708
WNT9B	LRP5	O75197	695
WNT9B	FZD5	Q13467	686
WNT9B	FZD7	O75084	648
WNT9B	FZD10	Q9ULW2	629
WNT9B	FZD4	Q9ULV1	620
WNT9B	AXIN2	Q9Y2T1	618
WNT9B	DKK1	O94907	616
WNT9B	PAX2	Q02962	608
WNT9B	CTNNB1	P35222	600
WNT9B	CITED1	Q99966	589
WNT9B	FZD6	O60353	587
WNT9B	LHX1	P48742	581
WNT9B	RSPO3	Q9BXY4	544

IntAct

6 interactions, top by confidence:

A	B	Type	Score
WNT9B	HSPA5	psi-mi:“MI:0915”(physical association)	0.400
WNT9B	ZMYM3	psi-mi:“MI:0915”(physical association)	0.400
WNT9B	AFM	psi-mi:“MI:0915”(physical association)	0.400
WNT9B	WLS	psi-mi:“MI:0915”(physical association)	0.400
WNT9B	ZZEF1	psi-mi:“MI:0914”(association)	0.350

BioGRID (14): HSPA5 (Affinity Capture-MS), ZZEF1 (Affinity Capture-MS), NDUFA2 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), ZZEF1 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), NDUFA2 (Affinity Capture-MS), HSPA5 (Proximity Label-MS), ZMYM3 (Proximity Label-MS), NDUFA2 (Affinity Capture-MS), HECTD3 (Affinity Capture-MS), ZZEF1 (Affinity Capture-MS), GUK1 (Cross-Linking-MS (XL-MS)), WNT9B (Affinity Capture-MS)

ESM2 similar proteins: A0M8S1, A0M8T2, A1X153, A4D7S0, A8XEH1, O14904, O14905, O35468, O42280, O70283, P09544, P21552, P22727, P28026, P28465, P51028, P51029, P51030, Q07DW8, Q07DX7, Q07DY7, Q07DZ8, Q07E18, Q07E31, Q07E44, Q09YI4, Q09YJ6, Q09YN1, Q108U2, Q27886, Q2IBB0, Q2IBB5, Q2IBE2, Q2IBF4, Q2IBG1, Q2QL85, Q2QLA5, Q2QLB6, Q2QLC7, Q2QLE7

Diamond homologs: A0M8S1, A0M8T2, A1X153, A4D7S0, O00744, O00755, O13267, O14905, O42122, O70283, O96014, P04426, P04628, P09544, P10108, P17553, P21551, P21552, P22724, P22725, P22726, P22727, P24257, P24383, P27467, P28047, P28465, P31285, P31286, P33945, P41221, P43446, P47793, P48614, P48615, P49337, P49338, P49339, P49340, P49893

SIGNOR signaling

5 interactions.

A	Effect	B	Mechanism
WNT9B	up-regulates	FZD3	binding
WNT9B	up-regulates	LRP5	binding
WNT9B	up-regulates	LRP6	binding
WNT9B	up-regulates	CHRNA1	binding
SOSTDC1	“down-regulates activity”	WNT9B

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

699 predictions. Top by Δscore:

Variant	Effect	Δscore
17:46872677:G:T	donor_gain	1.0000
17:46872750:G:T	donor_gain	1.0000
17:46872754:G:GT	donor_gain	1.0000
17:46875078:AT:A	acceptor_gain	1.0000
17:46875079:T:G	acceptor_gain	1.0000
17:46875079:T:TA	acceptor_gain	1.0000
17:46875086:G:A	acceptor_gain	1.0000
17:46875366:GGTG:G	donor_loss	1.0000
17:46875367:GTGA:G	donor_loss	1.0000
17:46876241:ACAG:A	acceptor_gain	1.0000
17:46876242:C:G	acceptor_gain	1.0000
17:46876242:CA:C	acceptor_loss	1.0000
17:46876243:A:AG	acceptor_gain	1.0000
17:46876243:AG:A	acceptor_gain	1.0000
17:46876243:AGGCT:A	acceptor_gain	1.0000
17:46876244:G:A	acceptor_loss	1.0000
17:46876244:G:GG	acceptor_gain	1.0000
17:46876244:GG:G	acceptor_gain	1.0000
17:46876244:GGC:G	acceptor_gain	1.0000
17:46876244:GGCT:G	acceptor_gain	1.0000
17:46876244:GGCTG:G	acceptor_gain	1.0000
17:46852375:GA:G	donor_gain	0.9900
17:46852377:G:GG	donor_gain	0.9900
17:46872515:A:AG	acceptor_gain	0.9900
17:46872516:G:GA	acceptor_gain	0.9900
17:46872649:G:GT	donor_gain	0.9900
17:46872697:GCT:G	donor_gain	0.9900
17:46872699:T:G	donor_gain	0.9900
17:46872699:T:TG	donor_gain	0.9900
17:46872705:GCC:G	donor_gain	0.9900

AlphaMissense

2287 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:46872733:G:C	W98C	1.000
17:46872733:G:T	W98C	1.000
17:46875243:G:C	W159C	1.000
17:46875243:G:T	W159C	1.000
17:46876319:G:C	W225C	1.000
17:46876319:G:T	W225C	1.000
17:46872704:T:A	C89S	0.999
17:46872705:G:C	C89S	0.999
17:46872731:T:A	W98R	0.999
17:46872731:T:C	W98R	0.999
17:46875127:G:C	A121P	0.999
17:46875140:C:A	A125D	0.999
17:46875170:G:A	C135Y	0.999
17:46875193:T:A	C143S	0.999
17:46875194:G:C	C143S	0.999
17:46875237:G:C	W157C	0.999
17:46875237:G:T	W157C	0.999
17:46875250:T:A	C162S	0.999
17:46875251:G:C	C162S	0.999
17:46875271:A:C	S169R	0.999
17:46875273:C:A	S169R	0.999
17:46875273:C:G	S169R	0.999
17:46875348:T:A	N194K	0.999
17:46875348:T:G	N194K	0.999
17:46876277:G:C	K211N	0.999
17:46876277:G:T	K211N	0.999
17:46876278:T:A	C212S	0.999
17:46876279:G:C	C212S	0.999
17:46876284:G:T	G214C	0.999
17:46876299:T:A	C219S	0.999

dbSNP variants (sampled 300 via entrez): RS1000012117 (17:46843449 ACT>A), RS1000017699 (17:46837221 G>A), RS1000051927 (17:46863818 C>A), RS1000067832 (17:46851356 G>C), RS1000095636 (17:46876937 G>C), RS1000292325 (17:46835065 G>A), RS1000306087 (17:46874605 T>A,G), RS1000465995 (17:46885602 C>T), RS1000519470 (17:46885889 T>C), RS1000541554 (17:46846902 G>A), RS1000605524 (17:46846250 T>A), RS1000652202 (17:46867564 G>A), RS1000685173 (17:46834843 C>T), RS1000715375 (17:46868097 G>A), RS1000746965 (17:46867888 TG>T)

Disease associations

OMIM: gene MIM:602864 | disease phenotypes:

GenCC curated gene-disease

Disease	Classification	Inheritance
renal agenesis	Moderate	Autosomal recessive

Mondo (1): renal agenesis (MONDO:0018470)

Orphanet (0):

HPO phenotypes

18 total (18 of 18 shown, HPO-id order):

HPO	Term
HP:0000008	Abnormal morphology of female internal genitalia
HP:0000104	Renal agenesis
HP:0000175	Cleft palate
HP:0000286	Epicanthus
HP:0000316	Hypertelorism
HP:0000369	Low-set ears
HP:0000457	Depressed nasal ridge
HP:0001562	Oligohydramnios
HP:0001563	Fetal polyuria
HP:0001958	Nonketotic hypoglycemia
HP:0002089	Pulmonary hypoplasia
HP:0002242	Abnormal intestine morphology
HP:0002575	Tracheoesophageal fistula
HP:0005107	Abnormal sacrum morphology
HP:0010497	Sirenomelia
HP:0030680	Abnormal cardiovascular system morphology
HP:0100335	Non-midline cleft of the upper lip
HP:0100589	Urogenital fistula

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST001613_8	Antineutrophil cytoplasmic antibody-associated vasculitis	9.000000e-06
GCST005580_141	Intraocular pressure	4.000000e-10
GCST005951_16	Body mass index	4.000000e-08
GCST010866_77	Coronary artery disease	2.000000e-10
GCST012218_1	Relapse in treatment-naive multiple sclerosis (time to event)	2.000000e-10
GCST012337_13	Nonsyndromic cleft lip with or without cleft palate	1.000000e-07

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004695	intraocular pressure measurement
EFO:0004340	body mass index
EFO:0004952	disease recurrence

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
propionaldehyde	decreases expression	1
ethyl-p-hydroxybenzoate	increases expression	1
arsenic disulfide	increases methylation	1
CGP 52608	affects binding, increases reaction	1
Resveratrol	affects cotreatment, decreases expression	1
Microplastics	increases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Pesticides	decreases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Polystyrenes	increases abundance, increases expression	1
Aflatoxin B1	decreases methylation	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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