B9D1

Summary

B9D1 (B9 domain containing 1, HGNC:24123) is a protein-coding gene on chromosome 17p11.2, encoding B9 domain-containing protein 1 (Q9UPM9). 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-containing protein, one of several that are involved in ciliogenesis. Alterations in expression of this gene have been found in a family with Meckel syndrome. Meckel syndrome has been associated with at least six different genes. This gene is located within the Smith-Magenis syndrome region on chromosome 17.

Source: NCBI Gene 27077 — RefSeq curated summary.

At a glance

• Gene–disease (curated): ciliopathy (Definitive, ClinGen) — +4 more curated relationships
• Clinical variants (ClinVar): 277 total — 7 pathogenic, 5 likely-pathogenic
• Phenotypes (HPO): 95
• Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
• MANE Select transcript: NM_015681

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24123
Approved symbol	B9D1
Name	B9 domain containing 1
Location	17p11.2
Locus type	gene with protein product
Status	Approved
Aliases	B9, EPPB9, MKS9, MKSR-1
Ensembl gene	ENSG00000108641
Ensembl biotype	protein_coding
OMIM	614144
Entrez	27077

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 17 protein_coding, 4 protein_coding_CDS_not_defined, 1 retained_intron, 1 nonsense_mediated_decay

ENST00000261499, ENST00000268841, ENST00000395616, ENST00000440841, ENST00000461069, ENST00000468679, ENST00000476298, ENST00000477478, ENST00000477683, ENST00000487415, ENST00000574508, ENST00000575478, ENST00000581122, ENST00000582857, ENST00000642870, ENST00000645021, ENST00000646248, ENST00000647056, ENST00000647252, ENST00000663089, ENST00000671102, ENST00000674596, ENST00000675510

RefSeq mRNA: 9 — MANE Select: NM_015681 NM_001321214, NM_001321215, NM_001321216, NM_001321217, NM_001321218, NM_001321219, NM_001330149, NM_001368769, NM_015681

CCDS: CCDS11205, CCDS82086, CCDS82087, CCDS82089, CCDS86584, CCDS92271, CCDS92272

Canonical transcript exons

ENST00000261499 — 7 exons

Exon	Start	End
ENSE00001809586	19343175	19343461
ENSE00003482041	19360320	19360388
ENSE00003484560	19343790	19343857
ENSE00003563922	19347269	19347331
ENSE00003595922	19347784	19347880
ENSE00003679607	19357840	19357951
ENSE00003873219	19362507	19362723

Expression profiles

Bgee: expression breadth ubiquitous, 224 present calls, max score 97.65.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.1646 / max 115.7689, expressed in 1706 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
164843	8.9632	1625
164842	7.1188	1457
164845	1.1425	691
164844	0.9401	492

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	97.65	gold quality
adenohypophysis	UBERON:0002196	96.64	gold quality
left testis	UBERON:0004533	96.23	gold quality
right testis	UBERON:0004534	95.77	gold quality
pituitary gland	UBERON:0000007	95.11	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	94.51	gold quality
bronchial epithelial cell	CL:0002328	94.43	gold quality
epithelium of bronchus	UBERON:0002031	94.36	gold quality
right lobe of thyroid gland	UBERON:0001119	93.97	gold quality
testis	UBERON:0000473	93.60	gold quality
left lobe of thyroid gland	UBERON:0001120	93.45	gold quality
bronchus	UBERON:0002185	93.43	gold quality
thyroid gland	UBERON:0002046	92.34	gold quality
nucleus accumbens	UBERON:0001882	91.85	gold quality
caudate nucleus	UBERON:0001873	91.21	gold quality
islet of Langerhans	UBERON:0000006	90.90	gold quality
right adrenal gland	UBERON:0001233	90.20	gold quality
metanephros cortex	UBERON:0010533	90.19	gold quality
putamen	UBERON:0001874	90.01	gold quality
right adrenal gland cortex	UBERON:0035827	90.00	gold quality
prefrontal cortex	UBERON:0000451	89.95	gold quality
right frontal lobe	UBERON:0002810	89.62	gold quality
left adrenal gland	UBERON:0001234	89.58	gold quality
left adrenal gland cortex	UBERON:0035825	89.32	gold quality
Brodmann (1909) area 9	UBERON:0013540	88.68	gold quality
body of pancreas	UBERON:0001150	88.49	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.44	gold quality
pancreas	UBERON:0001264	88.37	gold quality
body of uterus	UBERON:0009853	88.34	gold quality
endocervix	UBERON:0000458	88.12	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.89

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

13 targeting B9D1, 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-LET-7F-1-3P	100.00	74.02	3928
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-4447	99.85	67.81	2900
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-548O-3P	99.74	69.30	2228
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-146A-3P	99.13	68.99	1881
HSA-MIR-6886-3P	96.96	66.36	844
HSA-MIR-664B-5P	96.74	67.50	509
HSA-MIR-3672	94.46	65.67	646
HSA-MIR-6864-3P	94.46	65.97	625

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 5)

• Ciliary transition zone localization. Functions in a module with related proteins (MKS1 and B9D1) that cooperates with nephrocystins in ciliogenesis. (PMID:18337471)
• 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)
• B9D1 is a novel Meckel syndrome gene (PMID:21493627)
• describe four patients with mild Joubert phenotypes who carry pathogenic mutations in either MKS1 or B9D1, two genes previously implicated only in Meckel syndrome (PMID:24886560)
• Formation of the B9-domain protein complex MKS1-B9D2-B9D1 is essential as a diffusion barrier for ciliary membrane proteins. (PMID:32726168)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	b9d1	ENSDARG00000011727
mus_musculus	B9d1	ENSMUSG00000001039
rattus_norvegicus	B9d1	ENSRNOG00000002462
drosophila_melanogaster	B9d1	FBGN0038342
caenorhabditis_elegans		WBGENE00019364

Paralogs (2): MKS1 (ENSG00000011143), B9D2 (ENSG00000123810)

Protein

Protein identifiers

B9 domain-containing protein 1 — Q9UPM9 (reviewed: Q9UPM9)

Alternative names: MKS1-related protein 1

All UniProt accessions (17): Q9UPM9, A0A0B4J223, A0A2R8Y5M4, A0A2R8Y646, A0A2R8Y822, A0A2R8YD57, A0A2R8YFJ1, A0A590UJK9, A0A590UK40, A0A6Q8PFJ7, A0A6Q8PFN7, A8MYG7, H7C3B7, I3L126, I3L435, J3KSN2, J3QKN6

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. Required for ciliogenesis and sonic hedgehog/SHH signaling.

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

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

Disease relevance. Meckel syndrome 9 (MKS9) [MIM:614209] 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 27 (JBTS27) [MIM:617120] 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. JBTS27 inheritance is autosomal recessive. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the B9D family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9UPM9-1	1	yes
Q9UPM9-2	2

RefSeq proteins (9): NP_001308143, NP_001308144, NP_001308145, NP_001308146, NP_001308147, NP_001308148, NP_001317078, NP_001355698, NP_056496* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010796	C2_B9-type_dom	Family

Pfam: PF07162

UniProt features (9 total): sequence variant 5, chain 1, domain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9UPM9-F1	83.05	0.60

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: 365 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_TUMORAL_MACROPHAGE_DN, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, GOBP_EPITHELIUM_DEVELOPMENT, TGCGCANK_UNKNOWN, PAL_PRMT5_TARGETS_UP, GOBP_EMBRYONIC_DIGIT_MORPHOGENESIS, GOBP_PROTEIN_LOCALIZATION_TO_CILIUM, GOCC_MICROTUBULE_ORGANIZING_CENTER, MODULE_205, GOBP_IN_UTERO_EMBRYONIC_DEVELOPMENT, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, MODULE_285, SMID_BREAST_CANCER_LUMINAL_B_UP, GOBP_CILIUM_ORGANIZATION, GOBP_APPENDAGE_DEVELOPMENT

GO Biological Process (9): in utero embryonic development (GO:0001701), vasculature development (GO:0001944), smoothened signaling pathway (GO:0007224), regulation of protein localization (GO:0032880), embryonic digit morphogenesis (GO:0042733), camera-type eye development (GO:0043010), cilium assembly (GO:0060271), neuroepithelial cell differentiation (GO:0060563), cell projection organization (GO:0030030)

GO Molecular Function (2): hedgehog receptor activity (GO:0008158), protein binding (GO:0005515)

GO Cellular Component (11): centrosome (GO:0005813), cytosol (GO:0005829), axoneme (GO:0005930), membrane (GO:0016020), ciliary transition zone (GO:0035869), MKS complex (GO:0036038), ciliary basal body (GO:0036064), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), cell projection (GO:0042995)

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
cellular anatomical structure	6
microtubule organizing center	2
cilium	2
chordate embryonic development	1
system development	1
circulatory system development	1
cell surface receptor signaling pathway	1
intracellular protein localization	1
regulation of localization	1
embryonic limb morphogenesis	1
embryonic morphogenesis	1
eye development	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
columnar/cuboidal epithelial cell differentiation	1
cellular component organization	1
transmembrane signaling receptor activity	1
hedgehog family protein binding	1
binding	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

696 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
B9D1	TCTN1	Q2MV58	991
B9D1	CC2D2A	Q9P2K1	989
B9D1	TMEM67	Q5HYA8	987
B9D1	TCTN2	Q96GX1	982
B9D1	TMEM216	Q9P0N5	980
B9D1	TMEM231	Q9H6L2	978
B9D1	TCTN3	Q6NUS6	969
B9D1	B9D2	Q9BPU9	959
B9D1	CEP290	O15078	955
B9D1	MKS1	Q9NXB0	930
B9D1	NPHP1	O15259	927
B9D1	NPHP4	O75161	906
B9D1	TMEM237	Q96Q45	887
B9D1	AHI1	Q8N157	871
B9D1	RPGRIP1L	Q68CZ1	868

IntAct

32 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
MKS1	B9D2	psi-mi:“MI:0915”(physical association)	0.730
TCTN2	TCTN3	psi-mi:“MI:0914”(association)	0.640
B9D2	ANKRD40	psi-mi:“MI:0914”(association)	0.530
CC2D2A	OFD1	psi-mi:“MI:2364”(proximity)	0.420
TMEM231	TNFRSF10B	psi-mi:“MI:0914”(association)	0.350
TCTN2	TMEM131L	psi-mi:“MI:0914”(association)	0.350
BFSP1	RABGAP1L	psi-mi:“MI:0914”(association)	0.350
CCL4L1	QSOX1	psi-mi:“MI:0914”(association)	0.350
B9D2	PARN	psi-mi:“MI:0914”(association)	0.350
TCTN1	NPTX1	psi-mi:“MI:0914”(association)	0.350
TMEM231	WFS1	psi-mi:“MI:0914”(association)	0.350
TCTN1	GUSB	psi-mi:“MI:0914”(association)	0.350
TMEM17	ESYT2	psi-mi:“MI:2364”(proximity)	0.270
B9D2	RGPD3	psi-mi:“MI:2364”(proximity)	0.270
MKS1	GARRE1	psi-mi:“MI:2364”(proximity)	0.270
B9D1	TXNDC9	psi-mi:“MI:2364”(proximity)	0.270
B9D2	CKB	psi-mi:“MI:2364”(proximity)	0.270
MKS1	AIP	psi-mi:“MI:2364”(proximity)	0.270
B9D1	MKS1	psi-mi:“MI:0915”(physical association)	0.000
POSTN	B9D1	psi-mi:“MI:0915”(physical association)	0.000
B9D2	B9D1	psi-mi:“MI:0915”(physical association)	0.000
TMEM231	B9D1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (37): B9D1 (Affinity Capture-MS), B9D1 (Affinity Capture-MS), CCT2 (Proximity Label-MS), CCT3 (Proximity Label-MS), CCT4 (Proximity Label-MS), CCT5 (Proximity Label-MS), CCT6A (Proximity Label-MS), CCT7 (Proximity Label-MS), CCT8 (Proximity Label-MS), COQ6 (Proximity Label-MS), MTR (Proximity Label-MS), PDCL3 (Proximity Label-MS), PFDN4 (Proximity Label-MS), TCP1 (Proximity Label-MS), TXNDC9 (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: P0C5J2, Q503B7, Q5BJ61, Q6DFD7, Q9R1S0, Q9UPM9, Q9VF59, M9MRD5, P0C5J3, Q499Q5, Q56JY9, Q5SW45, Q9NXB0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 28 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	7	44.0×	9e-09
Cilium Assembly	6	36.2×	4e-07
Organelle biogenesis and maintenance	6	22.0×	5e-06

GO biological processes:

GO term	Partners	Fold	FDR
smoothened signaling pathway	5	33.6×	2e-05
cilium assembly	9	24.5×	1e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	7
Likely pathogenic	5
Uncertain significance	109
Likely benign	106
Benign	17

Top pathogenic / likely-pathogenic (12)

Variant ID	HGVS	Classification
1930287	NM_015681.6(B9D1):c.391C>T (p.Gln131Ter)	Pathogenic
2041948	NM_015681.6(B9D1):c.460G>T (p.Glu154Ter)	Pathogenic
2261381	NM_015681.6(B9D1):c.307dup (p.Tyr103fs)	Pathogenic
254680	NM_015681.6(B9D1):c.517GTG[1] (p.Val174del)	Pathogenic
3752879	NM_015681.6(B9D1):c.19del (p.Ser7fs)	Pathogenic
4793014	NM_015681.6(B9D1):c.403del (p.Ser135fs)	Pathogenic
635892	NM_015681.6(B9D1):c.285_341+154del	Pathogenic
1064604	NM_015681.6(B9D1):c.341G>A (p.Arg114Gln)	Likely pathogenic
1687049	NM_015681.6(B9D1):c.529G>C (p.Asp177His)	Likely pathogenic
2923503	NM_015681.6(B9D1):c.342-1G>T	Likely pathogenic
3763752	NM_015681.6(B9D1):c.472G>A (p.Val158Met)	Likely pathogenic
386519	NM_015681.6(B9D1):c.493G>T (p.Gly165Cys)	Likely pathogenic

SpliceAI

1672 predictions. Top by Δscore:

Variant	Effect	Δscore
17:19343854:CCAG:C	acceptor_gain	1.0000
17:19343855:CAG:C	acceptor_gain	1.0000
17:19343855:CAGC:C	acceptor_gain	1.0000
17:19343858:C:CC	acceptor_gain	1.0000
17:19357838:A:AC	donor_gain	1.0000
17:19357838:ACAG:A	donor_gain	1.0000
17:19357839:C:CC	donor_gain	1.0000
17:19357839:CAG:C	donor_gain	1.0000
17:19357839:CAGC:C	donor_gain	1.0000
17:19360319:CCG:C	donor_gain	1.0000
17:19360389:C:CC	acceptor_gain	1.0000
17:19347264:CTCA:C	donor_loss	0.9900
17:19347265:TCA:T	donor_loss	0.9900
17:19347266:CA:C	donor_loss	0.9900
17:19347328:GTGCC:G	acceptor_loss	0.9900
17:19347329:TGCCT:T	acceptor_loss	0.9900
17:19347331:CCTGA:C	acceptor_loss	0.9900
17:19347332:C:A	acceptor_loss	0.9900
17:19347332:C:CC	acceptor_gain	0.9900
17:19347777:GACCT:G	donor_loss	0.9900
17:19347778:ACCTA:A	donor_loss	0.9900
17:19347779:CCTA:C	donor_loss	0.9900
17:19347780:CTA:C	donor_loss	0.9900
17:19347781:TACCG:T	donor_loss	0.9900
17:19347782:A:AC	donor_gain	0.9900
17:19347782:A:AG	donor_loss	0.9900
17:19347782:ACCGG:A	donor_gain	0.9900
17:19347783:C:CC	donor_gain	0.9900
17:19347783:C:CG	donor_loss	0.9900
17:19347783:CCGG:C	donor_gain	0.9900

AlphaMissense

1336 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:19360334:A:G	W40R	1.000
17:19360334:A:T	W40R	1.000
17:19343441:C:G	G165R	0.999
17:19347307:A:C	F122L	0.999
17:19347307:A:T	F122L	0.999
17:19347309:A:G	F122L	0.999
17:19347814:C:T	G104E	0.999
17:19347815:C:A	G104W	0.999
17:19347820:C:T	G102D	0.999
17:19347821:C:G	G102R	0.999
17:19357840:A:G	W82R	0.999
17:19357840:A:T	W82R	0.999
17:19357856:G:C	S76R	0.999
17:19357856:G:T	S76R	0.999
17:19357858:T:G	S76R	0.999
17:19357888:A:G	W66R	0.999
17:19357888:A:T	W66R	0.999
17:19360332:C:A	W40C	0.999
17:19360332:C:G	W40C	0.999
17:19343434:A:T	V167D	0.998
17:19343810:G:T	A151D	0.998
17:19347302:G:T	P124Q	0.998
17:19347877:G:T	P83Q	0.998
17:19347878:G:A	P83S	0.998
17:19360333:C:G	W40S	0.998
17:19362526:C:T	G15E	0.998
17:19362527:C:A	G15W	0.998
17:19343440:C:T	G165D	0.997
17:19347815:C:G	G104R	0.997
17:19347815:C:T	G104R	0.997

dbSNP variants (sampled 300 via entrez): RS1000001515 (17:19366534 C>T), RS1000064244 (17:19374213 C>G,T), RS1000163565 (17:19347610 A>G,T), RS1000223798 (17:19377717 C>A,G,T), RS1000313705 (17:19352183 G>A), RS1000353346 (17:19352602 A>C,G), RS1000426060 (17:19362013 A>G), RS1000431344 (17:19345540 C>T), RS1000452092 (17:19361666 G>A,T), RS1000469331 (17:19349582 A>C), RS1000495556 (17:19376658 C>A,G), RS1000500293 (17:19349203 A>G), RS1000587610 (17:19357054 T>C), RS1000614911 (17:19345880 A>G), RS1000711662 (17:19340764 G>A)

Disease associations

OMIM: gene MIM:614144 | disease phenotypes: MIM:213300, MIM:249000, MIM:617120, MIM:614209, MIM:208500

GenCC curated gene-disease

Disease	Classification	Inheritance
Meckel syndrome, type 9	Strong	Autosomal recessive
Joubert syndrome 27	Strong	Autosomal recessive
ciliopathy	Strong	Autosomal recessive
Joubert syndrome	Supportive	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	Definitive	AR

Mondo (7): Joubert syndrome (MONDO:0018772), Meckel syndrome (MONDO:0018921), Joubert syndrome 27 (MONDO:0014927), Joubert syndrome and related disorders (MONDO:0015369), Meckel syndrome, type 9 (MONDO:0013630), ciliopathy (MONDO:0005308), Jeune syndrome (MONDO:0018770)

Orphanet (5): Isolated Joubert syndrome (Orphanet:475), Meckel syndrome (Orphanet:564), Joubert syndrome and related disorders (Orphanet:140874), Ciliopathy (Orphanet:363250), Jeune syndrome (Orphanet:474)

HPO phenotypes

95 total (30 of 95 shown, HPO-id order):

HPO	Term
HP:0000003	Multicystic kidney dysplasia
HP:0000007	Autosomal recessive inheritance
HP:0000028	Cryptorchidism
HP:0000037	Male pseudohermaphroditism
HP:0000062	Ambiguous genitalia
HP:0000068	Urethral atresia
HP:0000073	Ureteral duplication
HP:0000175	Cleft palate
HP:0000179	Thick lower lip vermilion
HP:0000202	Orofacial cleft
HP:0000221	Furrowed tongue
HP:0000238	Hydrocephalus
HP:0000252	Microcephaly
HP:0000276	Long face
HP:0000293	Full cheeks
HP:0000316	Hypertelorism
HP:0000325	Triangular face
HP:0000340	Sloping forehead
HP:0000347	Micrognathia
HP:0000358	Posteriorly rotated ears
HP:0000369	Low-set ears
HP:0000426	Prominent nasal bridge
HP:0000457	Depressed nasal ridge
HP:0000463	Anteverted nares
HP:0000482	Microcornea
HP:0000486	Strabismus
HP:0000488	Retinopathy
HP:0000508	Ptosis
HP:0000518	Cataract
HP:0000528	Anophthalmia

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C537571	Jeune syndrome (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression, increases expression	5
methylmercuric chloride	decreases expression	3
Cyclosporine	decreases expression, decreases methylation, increases expression	3
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
mercuric bromide	decreases expression, affects cotreatment	2
Arsenic	decreases expression, increases abundance, affects cotreatment	2
Benzo(a)pyrene	affects methylation, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Smoke	decreases expression, increases abundance, increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
aristolochic acid I	decreases expression	1
bisphenol A	decreases methylation	1
sodium arsenate	decreases expression, increases abundance	1
tris(2-butoxyethyl) phosphate	affects expression	1
beta-lapachone	decreases expression, increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
cobaltous chloride	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
aflatoxin B2	increases methylation	1
perfluorooctane sulfonic acid	increases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
ICG 001	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	increases expression	1
Vorinostat	increases expression	1
Leflunomide	decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Doxorubicin	decreases expression	1
Hydralazine	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00873678	Not specified	COMPLETED	Assessment of the Prevalence of Genes AHI1, NPHP1 and CEP290 in Joubert Syndrome
NCT01401998	Not specified	RECRUITING	ARPKD Database Study
NCT04874909	Not specified	COMPLETED	Classification, Functional Stratification and Biomarkers in Ciliopathy (CILLICORIRCM)
NCT00068224	Not specified	COMPLETED	Clinical and Molecular Investigations Into Ciliopathies
NCT00948376	Not specified	COMPLETED	Natural History of Asphyxiating Thoracic Dystrophy (DTJ)
NCT04143841	Not specified	TERMINATED	Viveye Ocular Magnetic Neurostimulation System (OMNS) for the Management of Severe Dry Eye Disease