U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    B9D1 B9 domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 27077, updated on 10-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    B9D1provided by HGNC
    Official Full Name
    B9 domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:24123
    See related
    Ensembl:ENSG00000108641 MIM:614144; AllianceGenome:HGNC:24123
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    B9; MKS9; EPPB9; MKSR1; JBTS27; MKSR-1
    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 genes. This gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Mar 2016]
    Expression
    Ubiquitous expression in brain (RPKM 7.5), testis (RPKM 6.3) and 25 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See B9D1 in Genome Data Viewer
    Location:
    17p11.2
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (19334695..19377913, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (19282742..19325948, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (19238008..19281226, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene epsin 2 Neighboring gene EPN2 intronic transcript 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8286 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:19189003-19189551 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:19192933-19193526 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11852 Neighboring gene EPN2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11853 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:19212235-19213151 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:19213152-19214067 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:19220479-19221018 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:19233317-19233511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:19234824-19235596 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11854 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11855 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:19237143-19237914 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8287 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:19244665-19245232 Neighboring gene Sharpr-MPRA regulatory region 2588 Neighboring gene microRNA 1180 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:19261015-19261514 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11856 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8288 Neighboring gene uncharacterized LOC105371573 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:19266095-19266879 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8289 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:19275949-19276498 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11858 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8291 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8292 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:19283774-19284736 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:19285982-19286482 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:19286483-19286983 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:19288791-19289336 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:19289337-19289882 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:19289883-19290428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:19294419-19295332 Neighboring gene mitogen-activated protein kinase 7 Neighboring gene microfibril associated protein 4 Neighboring gene uncharacterized LOC124903947

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. B9D1 is revealed as a novel Meckel syndrome (MKS) gene by targeted exon-enriched next-generation sequencing and deletion analysis. Hopp K, et al. Hum Mol Genet, 2011 Jul 1. PMID 21493627, Free PMC Article
    2. Formation of the B9-domain protein complex MKS1-B9D2-B9D1 is essential as a diffusion barrier for ciliary membrane proteins. Okazaki M, et al. Mol Biol Cell, 2020 Sep 15. PMID 32726168, Free PMC Article
    3. Mutations in B9D1 and MKS1 cause mild Joubert syndrome: expanding the genetic overlap with the lethal ciliopathy Meckel syndrome. Romani M, et al. Orphanet J Rare Dis, 2014 May 5. PMID 24886560, Free PMC Article
    4. Functional redundancy of the B9 proteins and nephrocystins in Caenorhabditis elegans ciliogenesis. Williams CL, et al. Mol Biol Cell, 2008 May. PMID 18337471, Free PMC Article
    5. Functional interactions between the ciliopathy-associated Meckel syndrome 1 (MKS1) protein and two novel MKS1-related (MKSR) proteins. Bialas NJ, et al. J Cell Sci, 2009 Mar 1. PMID 19208769, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Formation of the B9-domain protein complex MKS1-B9D2-B9D1 is essential as a diffusion barrier for ciliary membrane proteins.
      Title: Formation of the B9-domain protein complex MKS1-B9D2-B9D1 is essential as a diffusion barrier for ciliary membrane proteins.
    2. describe four patients with mild Joubert phenotypes who carry pathogenic mutations in either MKS1 or B9D1, two genes previously implicated only in Meckel syndrome
      Title: Mutations in B9D1 and MKS1 cause mild Joubert syndrome: expanding the genetic overlap with the lethal ciliopathy Meckel syndrome.
    3. B9D1 is a novel Meckel syndrome gene
      Title: B9D1 is revealed as a novel Meckel syndrome (MKS) gene by targeted exon-enriched next-generation sequencing and deletion analysis.
    4. Ciliary transition zone localization. Functions in a module with related proteins (MKS1 and B9D1) that cooperates with nephrocystins in ciliogenesis.
      Title: Functional redundancy of the B9 proteins and nephrocystins in Caenorhabditis elegans ciliogenesis.
    5. 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
      Title: Functional interactions between the ciliopathy-associated Meckel syndrome 1 (MKS1) protein and two novel MKS1-related (MKSR) proteins.
    Submit: New GeneRIF Correction

    Phenotypes

    Go to the top of the page Help

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Joubert syndrome 27
    MedGen: C4310706 OMIM: 617120 GeneReviews: Joubert Syndrome
    		not available
    Meckel syndrome, type 9
    MedGen: C3280155 OMIM: 614209 GeneReviews: Not available
    		not available

    Variation

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables hedgehog receptor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in camera-type eye development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cilium assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in embryonic digit morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuroepithelial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of protein localization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in smoothened signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in vasculature development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of MKS complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of MKS complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in ciliary basal body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in ciliary transition zone ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    B9 domain-containing protein 1
    Names
    B9 protein domain 1
    MKS1-related protein 1
    endothelial precursor protein B9

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_031885.2 RefSeqGene

      Range
      20471..40019
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_686

    mRNA and Protein(s)

    1. NM_001321214.2 → NP_001308143.1  B9 domain-containing protein 1 isoform d

      Status: REVIEWED

      Source sequence(s)
      AK293815, BI833202, HY047032
      Consensus CDS
      CCDS82087.1
      UniProtKB/TrEMBL
      A8MYG7, B4DEW0
      Related
      ENSP00000378978.3, ENST00000395616.7
      Conserved Domains (1) summary
      pfam07162
      Location:17 → 157
      B9-C2; Ciliary basal body-associated, B9 protein

    2. NM_001321215.3 → NP_001308144.1  B9 domain-containing protein 1 isoform e

      Status: REVIEWED

      Source sequence(s)
      AC124066, AK293815, HY047032
      Consensus CDS
      CCDS86584.1
      UniProtKB/TrEMBL
      A0A2R8Y646, B4DEW0
      Related
      ENSP00000495045.1, ENST00000647252.1
      Conserved Domains (1) summary
      pfam07162
      Location:17 → 158
      B9-C2; Ciliary basal body-associated, B9 protein

    3. NM_001321216.2 → NP_001308145.1  B9 domain-containing protein 1 isoform f

      Status: REVIEWED

      Source sequence(s)
      BC002944, HY047032
      Consensus CDS
      CCDS82089.1
      UniProtKB/TrEMBL
      A0A2R8Y5M4
      Related
      ENSP00000268841.6, ENST00000268841.10
      Conserved Domains (1) summary
      pfam07162
      Location:17 → 135
      B9-C2; Ciliary basal body-associated, B9 protein

    4. NM_001321217.2 → NP_001308146.1  B9 domain-containing protein 1 isoform g

      Status: REVIEWED

      Source sequence(s)
      AC124066, HY047032
      Consensus CDS
      CCDS82086.1
      UniProtKB/TrEMBL
      A0A0B4J223, B4DEW0
      Related
      ENSP00000433359.2, ENST00000461069.6
      Conserved Domains (1) summary
      pfam07162
      Location:17 → 157
      B9-C2; Ciliary basal body-associated, B9 protein

    5. NM_001321218.2 → NP_001308147.1  B9 domain-containing protein 1 isoform h

      Status: REVIEWED

      Source sequence(s)
      AB030506, AC124066, CA312151, HY047032
      UniProtKB/TrEMBL
      A0A590UK40
      Related
      ENSP00000499690.1, ENST00000671102.1
      Conserved Domains (1) summary
      pfam07162
      Location:17 → 159
      B9-C2; Ciliary basal body-associated, B9 protein

    6. NM_001321219.2 → NP_001308148.1  B9 domain-containing protein 1 isoform i

      Status: REVIEWED

      Source sequence(s)
      AB030506, AC124066, CA312151, HY047032
      Consensus CDS
      CCDS92272.1
      UniProtKB/TrEMBL
      A0A2R8Y5M4, A0A6Q8PFJ7
      Related
      ENSP00000501817.1, ENST00000675510.1
      Conserved Domains (1) summary
      pfam07162
      Location:17 → 139
      B9-C2; Ciliary basal body-associated, B9 protein

    7. NM_001330149.2 → NP_001317078.1  B9 domain-containing protein 1 isoform j

      Status: REVIEWED

      Source sequence(s)
      AC124066, BM129815, HY047032
      UniProtKB/TrEMBL
      B4DEW0
      Conserved Domains (1) summary
      pfam07162
      Location:17 → 157
      B9-C2; Ciliary basal body-associated, B9 protein

    8. NM_001368769.2 → NP_001355698.1  B9 domain-containing protein 1 isoform k

      Status: REVIEWED

      Source sequence(s)
      AC124066, AK309320
      Consensus CDS
      CCDS92271.1
      UniProtKB/TrEMBL
      J3QKN6
      Related
      ENSP00000463165.2, ENST00000582857.2
      Conserved Domains (1) summary
      pfam07162
      Location:1 → 39
      B9-C2; Ciliary basal body-associated, B9 protein

    9. NM_015681.6 → NP_056496.1  B9 domain-containing protein 1 isoform b

      See identical proteins and their annotated locations for NP_056496.1

      Status: REVIEWED

      Source sequence(s)
      AC124066
      Consensus CDS
      CCDS11205.1
      UniProtKB/Swiss-Prot
      Q9BU22, Q9UPM9
      Related
      ENSP00000261499.4, ENST00000261499.11
      Conserved Domains (1) summary
      pfam07162
      Location:17 → 173
      B9-C2; Ciliary basal body-associated, B9 protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      19334695..19377913 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047435756.1 → XP_047291712.1  B9 domain-containing protein 1 isoform X8

      UniProtKB/TrEMBL
      J3QKN6

    2. XM_047435750.1 → XP_047291706.1  B9 domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      B4DN64

    3. XM_047435753.1 → XP_047291709.1  B9 domain-containing protein 1 isoform X4

      UniProtKB/TrEMBL
      A0A590UK40

    4. XM_047435751.1 → XP_047291707.1  B9 domain-containing protein 1 isoform X2

      UniProtKB/Swiss-Prot
      Q9BU22, Q9UPM9

    5. XM_047435754.1 → XP_047291710.1  B9 domain-containing protein 1 isoform X5

      UniProtKB/TrEMBL
      B4DEW0

    6. XM_047435752.1 → XP_047291708.1  B9 domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      A8MYG7, B4DEW0

    7. XM_005256610.3 → XP_005256667.1  B9 domain-containing protein 1 isoform X7

      UniProtKB/TrEMBL
      A0A2R8Y5M4
      Related
      ENSP00000410835.1, ENST00000440841.1
      Conserved Domains (1) summary
      pfam07162
      Location:17 → 135
      B9-C2; Ciliary basal body-associated, B9 protein

    8. XM_047435755.1 → XP_047291711.1  B9 domain-containing protein 1 isoform X6

      UniProtKB/TrEMBL
      A0A2R8Y5M4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      19282742..19325948 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054315726.1 → XP_054171701.1  B9 domain-containing protein 1 isoform X8

      UniProtKB/TrEMBL
      J3QKN6

    2. XM_054315719.1 → XP_054171694.1  B9 domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      B4DN64

    3. XM_054315722.1 → XP_054171697.1  B9 domain-containing protein 1 isoform X4

      UniProtKB/TrEMBL
      A0A590UK40

    4. XM_054315720.1 → XP_054171695.1  B9 domain-containing protein 1 isoform X2

      UniProtKB/Swiss-Prot
      Q9BU22, Q9UPM9

    5. XM_054315723.1 → XP_054171698.1  B9 domain-containing protein 1 isoform X5

      UniProtKB/TrEMBL
      B4DEW0

    6. XM_054315721.1 → XP_054171696.1  B9 domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      A8MYG7, B4DEW0

    7. XM_054315725.1 → XP_054171700.1  B9 domain-containing protein 1 isoform X7

      UniProtKB/TrEMBL
      A0A2R8Y5M4

    8. XM_054315724.1 → XP_054171699.1  B9 domain-containing protein 1 isoform X6

      UniProtKB/TrEMBL
      A0A2R8Y5M4

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001243473.2: Suppressed sequence

      Description
      NM_001243473.2: This RefSeq was removed because currently there is support for the transcript but not for the protein.

    2. NM_001243475.2: Suppressed sequence

      Description
      NM_001243475.2: This RefSeq was removed because currently there is support for the transcript but not for the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UPM9.1 GenPept UniProtKB/Swiss-Prot:Q9UPM9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous