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

Gene ID: 27077, updated on 3-Apr-2024

Summary

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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
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Genomic context

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See B9D1 in Genome Data Viewer
Location:
17p11.2
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (19334695..19377913, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (19282742..19325948, complement)
105.20220307 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

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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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 (19) 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

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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
Compare labs
Meckel syndrome, type 9
MedGen: C3280155 OMIM: 614209 GeneReviews: Not available
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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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

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Preferred Names
B9 domain-containing protein 1
Names
B9 protein domain 1
MKS1-related protein 1
endothelial precursor protein B9

NCBI Reference Sequences (RefSeq)

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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_2023_10

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

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

  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

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

    UniProtKB/TrEMBL
    A8MYG7

  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

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

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

  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

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

    UniProtKB/TrEMBL
    A8MYG7

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

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

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

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