B9D2

Summary

B9D2 (B9 domain containing 2, HGNC:28636) is a protein-coding gene on chromosome 19q13.2, encoding B9 domain-containing protein 2 (Q9BPU9). Component of the tectonic-like complex, a complex localized at the transition zone of primary cilia and acting as a barrier that prevents diffusion of transmembrane proteins between the cilia and plasma membranes.

This gene encodes a B9 domain protein, which are exclusively found in ciliated organisms. The gene is upregulated during mucociliary differentiation, and the encoded protein localizes to basal bodies and cilia. Disrupting expression of this gene results in ciliogenesis defects.

Source: NCBI Gene 80776 — RefSeq curated summary.

At a glance

• Gene–disease (curated): Meckel syndrome, type 10 (Strong, GenCC) — +2 more curated relationships
• GWAS associations: 9
• Clinical variants (ClinVar): 111 total — 2 pathogenic, 5 likely-pathogenic
• Phenotypes (HPO): 96
• MANE Select transcript: NM_030578

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28636
Approved symbol	B9D2
Name	B9 domain containing 2
Location	19q13.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC4093, MKS10, MKSR-2
Ensembl gene	ENSG00000123810
Ensembl biotype	protein_coding
OMIM	611951
Entrez	80776

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000243578, ENST00000594416, ENST00000601597, ENST00000675972, ENST00000890348, ENST00000890349, ENST00000890350, ENST00000890351, ENST00000932334

RefSeq mRNA: 1 — MANE Select: NM_030578 NM_030578

CCDS: CCDS12579

Canonical transcript exons

ENST00000243578 — 4 exons

Exon	Start	End
ENSE00000842443	41354417	41355013
ENSE00001052862	41363958	41364149
ENSE00003465514	41357897	41358022
ENSE00003572078	41363432	41363523

Expression profiles

Bgee: expression breadth ubiquitous, 138 present calls, max score 88.51.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.7303 / max 77.5624, expressed in 1642 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
181057	3.4251	1547
181056	1.3052	562

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	88.51	gold quality
blood	UBERON:0000178	88.48	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	85.90	gold quality
granulocyte	CL:0000094	83.77	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	83.66	gold quality
monocyte	CL:0000576	83.65	gold quality
leukocyte	CL:0000738	83.53	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	82.68	gold quality
right adrenal gland	UBERON:0001233	81.54	gold quality
fallopian tube	UBERON:0003889	81.53	gold quality
bone marrow	UBERON:0002371	81.35	gold quality
right adrenal gland cortex	UBERON:0035827	80.76	gold quality
left adrenal gland	UBERON:0001234	80.42	gold quality
mucosa of transverse colon	UBERON:0004991	80.20	gold quality
left adrenal gland cortex	UBERON:0035825	79.92	gold quality
adult mammalian kidney	UBERON:0000082	79.40	gold quality
spleen	UBERON:0002106	79.38	gold quality
metanephros cortex	UBERON:0010533	78.59	gold quality
muscle layer of sigmoid colon	UBERON:0035805	78.56	gold quality
lower esophagus muscularis layer	UBERON:0035833	78.43	gold quality
lower esophagus	UBERON:0013473	78.39	gold quality
adrenal gland	UBERON:0002369	78.08	gold quality
left uterine tube	UBERON:0001303	77.94	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	77.92	gold quality
body of uterus	UBERON:0009853	77.81	gold quality
myometrium	UBERON:0001296	77.73	gold quality
cortex of kidney	UBERON:0001225	77.44	gold quality
body of stomach	UBERON:0001161	77.02	gold quality
right lobe of thyroid gland	UBERON:0001119	76.96	gold quality
transverse colon	UBERON:0001157	76.89	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-114	yes	11.16
E-ANND-3	yes	5.16

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

6 targeting B9D2, 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-6737-3P	98.95	68.56	1577
HSA-MIR-7157-3P	98.95	68.70	1582
HSA-MIR-6889-3P	98.84	67.35	1198
HSA-MIR-5008-3P	98.73	67.50	1433
HSA-MIR-6529-3P	98.68	66.76	1020
HSA-MIR-3691-5P	98.62	65.88	552

Literature-anchored findings (GeneRIF, showing 5)

• ICIS-1 is a new protein associated with ciliated cells and potentially related to cilia stability. This gene is localized within the TGF-beta1 promoter and is ubiquitously expressed in human tissues. (PMID:17127412)
• The ICIS-1 (Involved in CIlia Stability-1)gene is localized within the TGF-beta1 promoter and is upregulated during mucociliary differentiation. (PMID:17127412)
• MKS-1 and MKS-1-related proteins 1 and 2 (MKSR-1/EPPB9, MKSR-2/B9D2), localize to transition zones/basal bodies of sensory cilia; subcellular localization is largely co-dependent, pointing to a functional relationship between the proteins (PMID:19208769)
• Formation of the B9-domain protein complex MKS1-B9D2-B9D1 is essential as a diffusion barrier for ciliary membrane proteins. (PMID:32726168)
• New functions of B9D2 in tight junctions and epithelial polarity. (PMID:39455645)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	b9d2	ENSDARG00000017385
mus_musculus	B9d2	ENSMUSG00000063439
rattus_norvegicus	B9d2	ENSRNOG00000028753
drosophila_melanogaster	B9d2	FBGN0261683
caenorhabditis_elegans		WBGENE00021416

Paralogs (2): MKS1 (ENSG00000011143), B9D1 (ENSG00000108641)

Protein

Protein identifiers

B9 domain-containing protein 2 — Q9BPU9 (reviewed: Q9BPU9)

Alternative names: MKS1-related protein 2

All UniProt accessions (2): Q9BPU9, M0QY88

UniProt curated annotations — full annotation on UniProt →

Function. Component of the tectonic-like complex, a complex localized at the transition zone of primary cilia and acting as a barrier that prevents diffusion of transmembrane proteins between the cilia and plasma membranes.

Subunit / interactions. Part of the tectonic-like complex (also named B9 complex). Interacts with TUBG1.

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

Disease relevance. Meckel syndrome 10 (MKS10) [MIM:614175] A disorder characterized by a combination of renal cysts and variably associated features including developmental anomalies of the central nervous system (typically encephalocele), hepatic ductal dysplasia and cysts, and polydactyly. The disease is caused by variants affecting the gene represented in this entry. Joubert syndrome 34 (JBTS34) [MIM:614175] 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. JBTS34 inheritance is autosomal recessive. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the B9D family.

RefSeq proteins (1): NP_085055* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010796	C2_B9-type_dom	Family

Pfam: PF07162

UniProt features (8 total): sequence variant 6, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BPU9-F1	89.79	0.65

Function

Pathways and Gene Ontology

Reactome pathways

21 pathways

ID	Pathway
R-HSA-141444	Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal
R-HSA-2467813	Separation of Sister Chromatids
R-HSA-2500257	Resolution of Sister Chromatid Cohesion
R-HSA-5620912	Anchoring of the basal body to the plasma membrane
R-HSA-5663220	RHO GTPases Activate Formins
R-HSA-68877	Mitotic Prometaphase
R-HSA-9648025	EML4 and NUDC in mitotic spindle formation
R-HSA-141424	Amplification of signal from the kinetochores
R-HSA-162582	Signal Transduction
R-HSA-1640170	Cell Cycle
R-HSA-1852241	Organelle biogenesis and maintenance
R-HSA-194315	Signaling by Rho GTPases
R-HSA-195258	RHO GTPase Effectors
R-HSA-2555396	Mitotic Metaphase and Anaphase
R-HSA-5617833	Cilium Assembly
R-HSA-68882	Mitotic Anaphase
R-HSA-68886	M Phase
R-HSA-69278	Cell Cycle, Mitotic
R-HSA-69618	Mitotic Spindle Checkpoint
R-HSA-69620	Cell Cycle Checkpoints
R-HSA-9716542	Signaling by Rho GTPases, Miro GTPases and RHOBTB3

MSigDB gene sets: 330 (showing top): GOBP_PROTEIN_LOCALIZATION_TO_CILIUM, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_CILIUM_ORGANIZATION, GOCC_CENTROSOME, GOBP_ORGANELLE_ASSEMBLY, GGCKCATGS_UNKNOWN, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, RFX1_02, GOBP_CELL_PROJECTION_ORGANIZATION, TGTYNNNNNRGCARM_UNKNOWN, REACTOME_CELL_CYCLE_CHECKPOINTS, GOCC_CYTOPLASMIC_REGION, GOCC_CILIARY_TRANSITION_ZONE, MARSON_BOUND_BY_FOXP3_UNSTIMULATED

GO Biological Process (2): cilium assembly (GO:0060271), cell projection organization (GO:0030030)

GO Molecular Function (2): gamma-tubulin binding (GO:0043015), protein binding (GO:0005515)

GO Cellular Component (12): nucleus (GO:0005634), centrosome (GO:0005813), cytosol (GO:0005829), axoneme (GO:0005930), membrane (GO:0016020), MKS complex (GO:0036038), ciliary basal body (GO:0036064), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), ciliary transition zone (GO:0035869), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-14 pathways:

Category	Pathways
Mitotic Prometaphase	2
M Phase	2
Cell Cycle	2
Amplification of signal from the kinetochores	1
Mitotic Anaphase	1
Assembly of the 9+0 primary cilium	1
RHO GTPase Effectors	1
Mitotic Spindle Checkpoint	1
Signaling by Rho GTPases, Miro GTPases and RHOBTB3	1
Signaling by Rho GTPases	1
Organelle biogenesis and maintenance	1
Mitotic Metaphase and Anaphase	1
Cell Cycle, Mitotic	1
Cell Cycle Checkpoints	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	6
microtubule organizing center	2
cilium	2
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
cellular component organization	1
tubulin binding	1
binding	1
intracellular membrane-bounded organelle	1
centriole	1
cytoplasm	1
cytoskeleton	1
microtubule	1
ciliary plasm	1
protein-containing complex	1
ciliary transition zone	1
intracellular anatomical structure	1
intracellular membraneless organelle	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1

Protein interactions and networks

STRING

650 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
B9D2	TMEM67	Q5HYA8	975
B9D2	CC2D2A	Q9P2K1	969
B9D2	TMEM216	Q9P0N5	966
B9D2	B9D1	Q9UPM9	959
B9D2	TCTN1	Q2MV58	953
B9D2	TCTN2	Q96GX1	949
B9D2	TMEM231	Q9H6L2	943
B9D2	CEP290	O15078	895
B9D2	TCTN3	Q6NUS6	895
B9D2	NPHP1	O15259	886
B9D2	NPHP4	O75161	883
B9D2	TMEM237	Q96Q45	854
B9D2	AHI1	Q8N157	842
B9D2	RPGRIP1L	Q68CZ1	828
B9D2	TMEM17	Q86X19	826

IntAct

53 interactions, top by confidence:

A	B	Type	Score
B9D2	B9D1	psi-mi:“MI:0915”(physical association)	0.840
B9D2	TMEM231	psi-mi:“MI:0914”(association)	0.730
B9D2	MKS1	psi-mi:“MI:0915”(physical association)	0.730
MKS1	B9D2	psi-mi:“MI:0915”(physical association)	0.730
INVS	B9D2	psi-mi:“MI:0407”(direct interaction)	0.590
INVS	B9D2	psi-mi:“MI:0915”(physical association)	0.590
B9D2	INVS	psi-mi:“MI:0915”(physical association)	0.590
SPAG8	B9D2	psi-mi:“MI:0915”(physical association)	0.560
SAXO4	B9D2	psi-mi:“MI:0915”(physical association)	0.560
P4HA3	B9D2	psi-mi:“MI:0915”(physical association)	0.560
B9D2	VPS25	psi-mi:“MI:0915”(physical association)	0.560
TLX3	B9D2	psi-mi:“MI:0915”(physical association)	0.560
B9D2	ALKBH7	psi-mi:“MI:0915”(physical association)	0.560
PLEKHA7	B9D2	psi-mi:“MI:0915”(physical association)	0.560
QARS1	B9D2	psi-mi:“MI:0915”(physical association)	0.560
B9D2	ANKRD40	psi-mi:“MI:0914”(association)	0.530
IFT70B	B9D2	psi-mi:“MI:0407”(direct interaction)	0.530
B9D2	IFT70B	psi-mi:“MI:0915”(physical association)	0.530
CC2D2A	OFD1	psi-mi:“MI:2364”(proximity)	0.420
INVS	IFT70B	psi-mi:“MI:0915”(physical association)	0.400
TCTN1	PPOX	psi-mi:“MI:0914”(association)	0.350
TMEM231	TNFRSF10B	psi-mi:“MI:0914”(association)	0.350
B9D2	PARN	psi-mi:“MI:0914”(association)	0.350
TCTN1	GUSB	psi-mi:“MI:0914”(association)	0.350
TCTN1	NPTX1	psi-mi:“MI:0914”(association)	0.350

BioGRID (83): B9D2 (Affinity Capture-MS), ANP32A (Proximity Label-MS), ARID1B (Proximity Label-MS), B9D1 (Proximity Label-MS), BCOR (Proximity Label-MS), CNOT7 (Proximity Label-MS), CPSF7 (Proximity Label-MS), DCAF7 (Proximity Label-MS), DNMT1 (Proximity Label-MS), EIF4ENIF1 (Proximity Label-MS), FAM208A (Proximity Label-MS), FUBP3 (Proximity Label-MS), GRIP1 (Proximity Label-MS), HNRNPM (Proximity Label-MS), IBTK (Proximity Label-MS)

ESM2 similar proteins: A3QVV1, A7KAI6, B0JYW5, B0X2G0, B3M123, B3MZN7, B3NY19, B4JGX4, B4LZ60, B4NJR8, B4P925, B4PUG5, B4PYH5, B4QVL3, B5MCN3, M9MRD5, O08688, O15484, O88796, P0C5J2, P0C5J3, P78346, P78963, Q09541, Q22036, Q3SZ21, Q3UK10, Q503B7, Q56JY9, Q5BJ61, Q5S1W2, Q5XQC7, Q623S8, Q68EZ3, Q6DFD7, Q6DGZ1, Q6GN70, Q756G8, Q7QD36, Q8R4C0

Diamond homologs: M9MRD5, P0C5J3, Q3UK10, Q499Q5, Q56JY9, Q5SW45, Q6DGZ1, Q6GN70, Q9BPU9, Q9NXB0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 26 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
Anchoring of the basal body to the plasma membrane	5	35.3×	1e-05
Cilium Assembly	5	34.0×	1e-05
Organelle biogenesis and maintenance	5	20.6×	8e-05

GO biological processes:

GO term	Partners	Fold	FDR
cilium assembly	7	20.6×	5e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	5
Uncertain significance	50
Likely benign	32
Benign	10

Top pathogenic / likely-pathogenic (7)

Variant ID	HGVS	Classification
217557	NM_030578.4(B9D2):c.107T>C (p.Leu36Pro)	Pathogenic
30931	NM_030578.4(B9D2):c.301A>C (p.Ser101Arg)	Pathogenic
2501262	NM_030578.4(B9D2):c.223_224insT (p.Arg75fs)	Likely pathogenic
2501263	NM_030578.4(B9D2):c.33delinsTG (p.Ala13fs)	Likely pathogenic
4531724	NM_030578.4(B9D2):c.127C>T (p.Gln43Ter)	Likely pathogenic
684427	NM_030578.4(B9D2):c.15C>A (p.His5Gln)	Likely pathogenic
812149	NM_030578.4(B9D2):c.168C>G (p.Tyr56Ter)	Likely pathogenic

SpliceAI

711 predictions. Top by Δscore:

Variant	Effect	Δscore
19:41357892:CCCA:C	donor_loss	1.0000
19:41357893:CCA:C	donor_loss	1.0000
19:41357894:CA:C	donor_loss	1.0000
19:41357895:ACCTT:A	donor_loss	1.0000
19:41357896:C:A	donor_loss	1.0000
19:41361128:G:C	donor_gain	1.0000
19:41363971:A:C	donor_gain	1.0000
19:41357899:TGAAG:T	donor_gain	0.9900
19:41363467:T:A	donor_gain	0.9900
19:41363956:AC:A	donor_loss	0.9900
19:41363957:CCTT:C	donor_loss	0.9900
19:41363970:A:AC	donor_gain	0.9900
19:41364111:T:TA	donor_gain	0.9900
19:41355009:CCAGC:C	acceptor_gain	0.9800
19:41355010:CAGCC:C	acceptor_gain	0.9800
19:41355013:CCTG:C	acceptor_loss	0.9800
19:41355014:C:CC	acceptor_gain	0.9800
19:41355014:CT:C	acceptor_loss	0.9800
19:41355015:T:G	acceptor_loss	0.9800
19:41358018:CGCCC:C	acceptor_gain	0.9800
19:41358019:GCCCC:G	acceptor_loss	0.9800
19:41358022:CCT:C	acceptor_loss	0.9800
19:41358023:CTGC:C	acceptor_loss	0.9800
19:41358024:T:A	acceptor_loss	0.9800
19:41363995:A:AT	donor_gain	0.9800
19:41364027:T:TA	donor_gain	0.9800
19:41355010:CAGC:C	acceptor_gain	0.9700
19:41355011:AGC:A	acceptor_gain	0.9700
19:41355012:GC:G	acceptor_gain	0.9700
19:41355013:CC:C	acceptor_gain	0.9700

AlphaMissense

1135 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:41358014:A:G	W33R	0.999
19:41358014:A:T	W33R	0.999
19:41354944:C:T	G95E	0.998
19:41355011:A:G	W73R	0.998
19:41355011:A:T	W73R	0.998
19:41357942:A:G	W57R	0.998
19:41357942:A:T	W57R	0.998
19:41357980:G:T	T44K	0.997
19:41358012:C:A	W33C	0.997
19:41358012:C:G	W33C	0.997
19:41363451:G:C	C23W	0.997
19:41363497:C:T	G8E	0.997
19:41354889:C:A	W113C	0.996
19:41354889:C:G	W113C	0.996
19:41354891:A:G	W113R	0.996
19:41354891:A:T	W113R	0.996
19:41363447:A:G	W25R	0.996
19:41363447:A:T	W25R	0.996
19:41363453:A:G	C23R	0.996
19:41354977:T:A	D84V	0.995
19:41355007:G:T	P74H	0.995
19:41357929:A:T	I61N	0.995
19:41357980:G:C	T44R	0.995
19:41363452:C:T	C23Y	0.995
19:41363498:C:A	G8W	0.995
19:41354945:C:G	G95R	0.994
19:41354945:C:T	G95R	0.994
19:41363472:G:C	F16L	0.994
19:41363472:G:T	F16L	0.994
19:41363474:A:G	F16L	0.994

dbSNP variants (sampled 300 via entrez): RS1000123002 (19:41357866 G>A), RS1000244786 (19:41359860 C>A,T), RS1000405912 (19:41357604 G>A), RS1000438828 (19:41354191 G>A), RS1000722238 (19:41359627 C>T), RS1000751328 (19:41363917 C>A,G,T), RS1001044338 (19:41365110 T>A), RS1001473424 (19:41355221 A>G), RS1001651288 (19:41361470 C>T), RS1002083193 (19:41358220 C>A,T), RS1002187622 (19:41366083 C>A,T), RS1002262750 (19:41362078 C>A), RS1002859308 (19:41365331 C>T), RS1002911678 (19:41365519 C>G), RS1003312364 (19:41360284 T>C)

Disease associations

OMIM: gene MIM:611951 | disease phenotypes: MIM:213300, MIM:249000, MIM:614175

GenCC curated gene-disease

Disease	Classification	Inheritance
Meckel syndrome, type 10	Strong	Autosomal recessive
ciliopathy	Strong	Autosomal recessive
Meckel syndrome	Supportive	Autosomal recessive

ClinGen Gene-Disease Validity (1)

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

Disease	Classification	Inheritance
ciliopathy	Moderate	AR

Mondo (6): Joubert syndrome (MONDO:0018772), Meckel syndrome (MONDO:0018921), Meckel syndrome, type 10 (MONDO:0013609), ciliopathy (MONDO:0005308), Joubert syndrome and related disorders (MONDO:0015369), Joubert syndrome 34 (MONDO:0800383)

Orphanet (4): Isolated Joubert syndrome (Orphanet:475), Meckel syndrome (Orphanet:564), Ciliopathy (Orphanet:363250), Joubert syndrome and related disorders (Orphanet:140874)

HPO phenotypes

96 total (30 of 96 shown, HPO-id order):

HPO	Term
HP:0000003	Multicystic kidney dysplasia
HP:0000007	Autosomal recessive inheritance
HP:0000028	Cryptorchidism
HP:0000037	Male pseudohermaphroditism
HP:0000047	Hypospadias
HP:0000054	Micropenis
HP:0000062	Ambiguous genitalia
HP:0000068	Urethral atresia
HP:0000073	Ureteral duplication
HP:0000107	Renal cyst
HP:0000175	Cleft palate
HP:0000193	Bifid uvula
HP:0000202	Orofacial cleft
HP:0000221	Furrowed tongue
HP:0000238	Hydrocephalus
HP:0000252	Microcephaly
HP:0000276	Long face
HP:0000286	Epicanthus
HP:0000293	Full cheeks
HP:0000316	Hypertelorism
HP:0000340	Sloping forehead
HP:0000347	Micrognathia
HP:0000358	Posteriorly rotated ears
HP:0000369	Low-set ears
HP:0000377	Abnormal pinna morphology
HP:0000426	Prominent nasal bridge
HP:0000457	Depressed nasal ridge
HP:0000463	Anteverted nares
HP:0000482	Microcornea
HP:0000486	Strabismus

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST002454_12	Colorectal cancer	1.000000e-08
GCST004898_3	Preterm birth (maternal effect)	5.000000e-07
GCST005194_185	Coronary artery disease	4.000000e-17
GCST005195_126	Coronary artery disease	2.000000e-17
GCST005196_238	Coronary artery disease	4.000000e-16
GCST007096_256	Pulse pressure	2.000000e-08
GCST007856_49	Colorectal cancer or advanced adenoma	1.000000e-06
GCST010480_17	Coronary artery disease	7.000000e-09
GCST010480_23	Coronary artery disease	9.000000e-09

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0003917	premature birth
EFO:0005939	parental genotype effect measurement
EFO:0005763	pulse pressure measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

Variant	Genes	Level	Score	#Clin annots	Drugs
rs1800469	B9D2, TGFB1, TMEM91	3	2.50	2	aspirin;irinotecan

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	increases abundance, increases expression, decreases expression	2
Smoke	decreases expression, increases abundance, increases expression	2
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
2,6-dichloro-(1,4)benzoquinone	increases expression	1
Temozolomide	increases expression	1
Arsenic	affects methylation	1
Benzo(a)pyrene	increases methylation	1
Rotenone	decreases expression	1
Dronabinol	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Antirheumatic Agents	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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

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