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

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

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Ciliopathy	Conflicting classifications of pathogenicity	rs886038205, rs145712777	RCV005361490 RCV005367354
Jeune thoracic dystrophy	Conflicting classifications of pathogenicity	rs886038205	RCV000754944
Ovarian serous cystadenocarcinoma	Uncertain significance	rs771997194	RCV005895362
Uterine corpus endometrial carcinoma	Conflicting classifications of pathogenicity	rs73980009	RCV005900775

Associations from Text Mining
Disease Name	Relationship Type	References
Agenesis of Cerebellar Vermis	Associate	24886560
Ciliopathies	Associate	24886560
Glycosuria Renal	Associate	34338422
Meckel syndrome type 1	Associate	21493627, 24886560, 25920555