B9D1 (B9 domain containing 1)

Gene

• Entrez ID: 27077
• Gene name: B9 domain containing 1
• Gene symbol: B9D1
• Synonyms (NCBI Gene): B9, EPPB9, JBTS27, MKS9, MKSR-1, MKSR1
• Chromosome: 17
• Chromosome location: 17p11.2
• Summary: 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 ge

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs143149764	A>G	Likely-pathogenic, pathogenic	Splice donor variant
rs201299216	A>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Coding sequence variant, missense variant
rs369488112	G>A	Pathogenic	Intron variant, synonymous variant, genic downstream transcript variant, coding sequence variant, missense variant
rs373478202	G>A,C,T	Pathogenic, uncertain-significance	Synonymous variant, stop gained, coding sequence variant, missense variant, 5 prime UTR variant
rs771170000	T>C	Pathogenic, uncertain-significance	5 prime UTR variant, missense variant, coding sequence variant
rs886038205	C>G,T	Uncertain-significance, pathogenic	Missense variant, genic downstream transcript variant, coding sequence variant, intron variant
rs886038206	CAC>-	Pathogenic	Inframe deletion, genic downstream transcript variant, coding sequence variant, 3 prime UTR variant, intron variant, downstream transcript variant
rs886039811	A>G	Likely-pathogenic	Missense variant, coding sequence variant, 5 prime UTR variant, synonymous variant
rs1057522520	C>A,G	Likely-pathogenic	Intron variant, genic downstream transcript variant, missense variant, coding sequence variant, 3 prime UTR variant, downstream transcript variant
rs1598057395	ATACAGGCTACAACCCCCCTGGCCACCAGGCTGAGCTGCCCAGGCCCCTGGAGACCCCAGAGCATTCCCAGCCTGAACCTAAGACAGAAAACGAGGTGAAGTCTGTCCTAGGACAAGTCCTGCCCAGGGCCCAGGTCAGAATGAGGACCTACCGGCCAGGTGAGAAGGGCACGTGCACGGCCCCATAGCCTCGAACCACATCGTTCCCGAA>-	Pathogenic	5 prime UTR variant, coding sequence variant, intron variant, splice donor variant

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001701	Process	In utero embryonic development	IEA
GO:0001944	Process	Vasculature development	IEA
GO:0005515	Function	Protein binding	IPI	26638075, 27173435, 32726168, 33961781
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IDA	19208769
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005929	Component	Cilium	IEA
GO:0007224	Process	Smoothened signaling pathway	IEA
GO:0007224	Process	Smoothened signaling pathway	ISS
GO:0008158	Function	Hedgehog receptor activity	IEA
GO:0008158	Function	Hedgehog receptor activity	ISS
GO:0016020	Component	Membrane	IEA
GO:0030030	Process	Cell projection organization	IEA
GO:0032880	Process	Regulation of protein localization	IEA
GO:0035869	Component	Ciliary transition zone	IEA
GO:0035869	Component	Ciliary transition zone	ISS
GO:0036038	Component	MKS complex	IBA
GO:0036038	Component	MKS complex	IEA
GO:0036038	Component	MKS complex	ISS
GO:0036064	Component	Ciliary basal body	IDA	19208769
GO:0042733	Process	Embryonic digit morphogenesis	IEA
GO:0042995	Component	Cell projection	IEA
GO:0043010	Process	Camera-type eye development	IEA
GO:0060271	Process	Cilium assembly	IBA
GO:0060271	Process	Cilium assembly	IEA
GO:0060271	Process	Cilium assembly	ISS
GO:0060563	Process	Neuroepithelial cell differentiation	IEA

Other IDs

• MIM: 614144
• HGNC: 24123
• e!Ensembl: ENSG00000108641

Protein

• UniProt ID: Q9UPM9
• Protein name: B9 domain-containing protein 1 (MKS1-related protein 1)
• Protein 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 s
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF07162	B9-C2	11 → 174	Ciliary basal body-associated, B9 protein	Domain

• Sequence:

  MATASPSVFLLMVNGQVESAQFPEYDDLYCKYCFVYGQDWAPTAGLEEGISQITSKSQDV
  RQALVWNFPIDVTFKSTNPYGWPQIVLSVYGPDVFGNDVVRGYGAVHVPFSPGRHKRTIP
  MFVPESTSKLQKFTSWFMGRRPEYTDPKVVAQGEGREVTRVRSQGFVTLLFNVVTKDMRK
  LGYDTGPSDTQGVLGPSPPQSFPQ

• Sequence length: 204

Pathways

Reactome:

Anchoring of the basal body to the plasma membrane

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
B9D1-related disorder	Likely pathogenic	rs778260923	RCV004734157	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Glioma susceptibility 1	Likely pathogenic	rs778260923	RCV005912568	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Joubert syndrome	Likely pathogenic; Pathogenic	rs778260923, rs1462645325, rs1908307291, rs369488112, rs1908964770, rs143149764	RCV001871960 RCV002626749 RCV002903368 RCV000201564 RCV003780621 RCV000818541	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Joubert syndrome 27	Likely pathogenic; Pathogenic	rs778260923, rs1309922077, rs369488112, rs886038206, rs143149764	RCV001726509 RCV002248480 RCV004796098 RCV000241542 RCV001270058	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Joubert syndrome and related disorders	Likely pathogenic	rs778260923	RCV003230666	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Meckel syndrome, type 9	Likely pathogenic; Pathogenic	rs1309922077, rs143149764	RCV002248480 RCV000024098	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Meckel-Gruber syndrome	Likely pathogenic; Pathogenic	rs778260923, rs1462645325, rs1908307291, rs1908964770, rs143149764, rs1598057395	RCV001871960 RCV002626749 RCV002903368 RCV003780621 RCV000818541 RCV000787398	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CILIOPATHIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ciliopathy	Conflicting classifications of pathogenicity	ClinVar ClinGen, GWAS catalog	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
CONGENITAL CYSTIC KIDNEY DISEASE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FAMILIAL APLASIA OF THE VERMIS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTROINTESTINAL STROMAL TUMORS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ISOLATED JOUBERT SYNDROME	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Jeune thoracic dystrophy	Conflicting classifications of pathogenicity	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
LIVER CIRRHOSIS, EXPERIMENTAL	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MECKEL SYNDROME	—	GWAS catalog, Orphanet GWAS catalog, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Agenesis of corpus callosum	Agenesis Of Corpus Callosum	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Ambiguous Genitalia	Ambiguous Genitalia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Anencephaly	Anencephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Anophthalmos	Syndromic microphthalmia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Aplasia Cutis Congenita	Aplasia Cutis Congenita	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Blepharoptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ciliopathies	Ciliopathies	GENOMICS_ENGLAND_DG	21493627, 24886560, 25920555		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ciliopathies	Ciliopathies	BEFREE	24886560		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ciliopathies	Ciliopathy	Pubtator	24886560	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital absence of spleen	Asplenia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital cerebral hernia	Congenital Cerebral Hernia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital clubfoot	Congenital Clubfoot	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital coloboma of iris	Congenital Coloboma Of Iris	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cystic liver disease	Cystic liver disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dandy-Walker Syndrome	Dandy-Walker Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Double ureter	Double Ureter	HPO_DG			★☆☆☆☆ Found in Text Mining only
Familial aplasia of the vermis	Cerebellar vermis agenesis	CLINVAR_DG	21493627, 26092869		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial aplasia of the vermis	Cerebellar vermis agenesis	ORPHANET_DG	24886560		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Fibrosis of pancreas	Fibrosis Of Pancreas	HPO_DG			★☆☆☆☆ Found in Text Mining only
Gastrointestinal Stromal Sarcoma	Gastrointestinal stromal tumor	CTD_human_DG	27793025		★☆☆☆☆ Found in Text Mining only
Gastrointestinal Stromal Tumors	Gastrointestinal stromal tumor	CTD_human_DG	27793025		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glycosuria Renal	Renal glycosuria	Pubtator	34338422	Associate	★☆☆☆☆ Found in Text Mining only
Hepatic Fibrosis, Congenital	Congenital Hepatic Fibrosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hirschsprung Disease	Hirschsprung Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hydrocephalus	Hydrocephalus	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Joubert syndrome	Joubert syndrome	Orphanet			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Joubert syndrome 1	Joubert Syndrome	ORPHANET_DG	24886560		★☆☆☆☆ Found in Text Mining only
JOUBERT SYNDROME 27	Joubert Syndrome	GENOMICS_ENGLAND_DG	21493627, 24886560, 25920555		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
JOUBERT SYNDROME 27	Joubert Syndrome	UNIPROT_DG	24886560		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
JOUBERT SYNDROME 27	Joubert Syndrome	CLINVAR_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Liver neoplasms	Liver neoplasms	BEFREE	27956228		★☆☆☆☆ Found in Text Mining only
Lobar Holoprosencephaly	Lobar Holoprosencephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Male Pseudohermaphroditism	Male Pseudohermaphroditism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of liver	Liver Cancer	BEFREE	27956228		★☆☆☆☆ Found in Text Mining only
Meckel syndrome	Meckel Syndrome	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Meckel syndrome type 1	Meckel Syndrome	BEFREE	21493627, 21763481, 24886560, 25920555		★☆☆☆☆ Found in Text Mining only
Meckel syndrome type 1	Meckel Syndrome	GENOMICS_ENGLAND_DG	21493627, 24886560, 25920555		★☆☆☆☆ Found in Text Mining only
Meckel syndrome type 1	Meckel-gruber syndrome	Pubtator	21493627, 24886560, 25920555	Associate	★☆☆☆☆ Found in Text Mining only
MECKEL SYNDROME, TYPE 9	Meckel Syndrome	GENOMICS_ENGLAND_DG	21493627, 24886560, 25920555		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
MECKEL SYNDROME, TYPE 9	Meckel Syndrome	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Meckel-Gruber syndrome	Meckel-Gruber Syndrome	ORPHANET_DG	21493627		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Meckel-Gruber syndrome	Meckel-Gruber Syndrome	CLINVAR_DG	21493627		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Meckel-Gruber syndrome	Meckel-Gruber Syndrome	BEFREE	25920555		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microcornea	Microcornea	HPO_DG			★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microphthalmos	Microphthalmos	HPO_DG			★☆☆☆☆ Found in Text Mining only
Multicystic Dysplastic Kidney	Multicystic renal dysplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	27956228		★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Occipital Encephalocele	Occipital Encephalocele	HPO_DG			★☆☆☆☆ Found in Text Mining only
Occipital Encephalocele	Occipital Encephalocele	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Oculomotor apraxia	Oculomotor apraxia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Oculovestibuloauditory syndrome	Oculovestibuloauditory Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Oral cleft	Oral cleft	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pancreatic Cyst	Pancreatic Cyst	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polycystic liver disease	Polycystic liver disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polydactyly	Polydactyly	BEFREE	21763481		★☆☆☆☆ Found in Text Mining only
Polydactyly	Polydactyly	GENOMICS_ENGLAND_DG	24886560		★☆☆☆☆ Found in Text Mining only
Polydactyly	Polydactyly	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Polydactyly of toes	Polydactyly Of Toes	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polydactyly preaxial type 1	Polydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polymicrogyria	Polymicrogyria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Postaxial foot polydactyly	Foot Polydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	GWASCAT_DG	27846195		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sclerocornea	Sclerocornea	HPO_DG			★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Situs inversus totalis	Situs Inversus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Talipes	Talipes	HPO_DG			★☆☆☆☆ Found in Text Mining only
True Hermaphroditism (disorder)	True Hermaphroditism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ulnar polydactyly of fingers	Postaxial hand polydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Urethral atresia	Urethral atresia	HPO_DG			★☆☆☆☆ Found in Text Mining only