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B9D1 Gene(Protein Coding)

B9 Domain Containing 1

GCID:
GC17M019244
GIFtS:
44
Genes Participants
UDN Logo

Aliases for B9D1 Gene

Aliases for B9D1 Gene

  • B9 Domain Containing 1 2 3 5
  • Endothelial Precursor Protein B9 2 3
  • MKS1-Related Protein 1 3 4
  • B9 Protein Domain 1 2 3
  • MKSR1 3 4
  • B9 Domain-Containing Protein 1 3
  • JBTS27 3
  • EPPB9 3
  • MKS9 3
  • B9 3

External Ids for B9D1 Gene

Previous GeneCards Identifiers for B9D1 Gene

  • GC17M019188
  • GC17M018626

Summaries for B9D1 Gene

Entrez Gene Summary for B9D1 Gene

  • 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]

GeneCards Summary for B9D1 Gene

B9D1 (B9 Domain Containing 1) is a Protein Coding gene. Diseases associated with B9D1 include Joubert Syndrome 27 and Meckel Syndrome, Type 9. Among its related pathways are Organelle biogenesis and maintenance and Regulation of PLK1 Activity at G2/M Transition. Gene Ontology (GO) annotations related to this gene include hedgehog receptor activity. An important paralog of this gene is B9D2.

UniProtKB/Swiss-Prot for B9D1 Gene

  • 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 (By similarity).

Additional gene information for B9D1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for B9D1 Gene

Genomics for B9D1 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for B9D1 Gene

Promoters and enhancers for B9D1 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH17I019376 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 550.8 0.0 -37 3.7 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B YY1 POLR2B MAPK7 B9D1 ENSG00000262202 EPN2 AKAP10 FOXO3B FAM106A ENSG00000235979 ENSG00000230197 MFAP4
GH17I019361 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.4 +15.7 15710 2.3 CLOCK ARID4B SIN3A DMAP1 ZNF2 ZBTB7B IRF4 YY1 SLC30A9 POLR2B LOC105371573 B9D1 EPN2 MFAP4 SLC47A1 FAM83G TVP23B ENSG00000252349 ENSG00000262202 LOC102724624
GH17I018857 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE 9.7 +518.8 518812 3.8 HDGF PKNOX1 MLX ARID4B SIN3A IRF4 YY1 ZNF121 GLIS2 ZNF207 PRPSAP2 TVP23B ENSG00000231625 LOC645139 B9D1 FOXO3B ENSG00000264273 RN7SL627P LOC101929141
GH17I019336 Enhancer 1.3 Ensembl ENCODE dbSUPER 11.2 +40.0 40025 3.4 FOXA2 MLX ZFP64 ARID4B DMAP1 ZNF48 ETS1 YY1 ZNF143 ATF7 EPN2 ENSG00000262319 ENSG00000262292 MAPK7 B9D1 MFAP4 ENSG00000252349 ENSG00000265263 PIR55134
GH17I019726 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 9.7 -349.6 -349638 3.1 FOXA2 NFIB RAD21 YY1 ZNF335 ZNF23 RCOR1 ATF7 EGR2 ZNF362 UPF3AP2 ENSG00000252349 ALDH3A2 SLC47A1 PRPSAP2 B9D1 SLC47A2 ALDH3A1 MAPK7 ENSG00000262681
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around B9D1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the B9D1 gene promoter:

Genomic Locations for B9D1 Gene

Genomic Locations for B9D1 Gene
chr17:19,335,263-19,378,182
(GRCh38/hg38)
Size:
42,920 bases
Orientation:
Minus strand
chr17:19,240,867-19,281,495
(GRCh37/hg19)

Genomic View for B9D1 Gene

Genes around B9D1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
B9D1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for B9D1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for B9D1 Gene

Proteins for B9D1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for B9D1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9UPM9-B9D1_HUMAN
    Recommended name:
    B9 domain-containing protein 1
    Protein Accession:
    Q9UPM9
    Secondary Accessions:
    • Q9BU22

    Protein attributes for B9D1 Gene

    Size:
    204 amino acids
    Molecular mass:
    22775 Da
    Quaternary structure:
    • Part of the tectonic-like complex (also named B9 complex).

    Alternative splice isoforms for B9D1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for B9D1 Gene

Post-translational modifications for B9D1 Gene

Other Protein References for B9D1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for B9D1 Gene

Domains & Families for B9D1 Gene

Gene Families for B9D1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted secreted proteins

Protein Domains for B9D1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for B9D1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9UPM9

UniProtKB/Swiss-Prot:

B9D1_HUMAN :
  • Belongs to the B9D family.
Family:
  • Belongs to the B9D family.
genes like me logo Genes that share domains with B9D1: view

Function for B9D1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for B9D1 Gene

UniProtKB/Swiss-Prot 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 (By similarity).

Phenotypes From GWAS Catalog for B9D1 Gene

Gene Ontology (GO) - Molecular Function for B9D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008158 hedgehog receptor activity ISS --
genes like me logo Genes that share ontologies with B9D1: view
genes like me logo Genes that share phenotypes with B9D1: view

Human Phenotype Ontology for B9D1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for B9D1 Gene

MGI Knock Outs for B9D1:
  • B9d1 tm1d(EUCOMM)Wtsi
  • B9d1 tm1a(EUCOMM)Wtsi

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for B9D1 Gene

Localization for B9D1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for B9D1 Gene

Cytoplasm, cytoskeleton, cilium basal body. Cytoplasm, cytoskeleton, cilium axoneme. Note=Localizes at the transition zone, a region between the basal body and the ciliary axoneme. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for B9D1 gene
Compartment Confidence
cytoskeleton 5
cytosol 5
extracellular 3
nucleus 2

Gene Ontology (GO) - Cellular Components for B9D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005813 centrosome IDA 19208769
GO:0005829 cytosol TAS --
GO:0005856 cytoskeleton IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with B9D1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for B9D1 Gene

Pathways & Interactions for B9D1 Gene

genes like me logo Genes that share pathways with B9D1: view

Pathways by source for B9D1 Gene

Gene Ontology (GO) - Biological Process for B9D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001701 in utero embryonic development IEA --
GO:0001944 vasculature development IEA --
GO:0007224 smoothened signaling pathway ISS --
GO:0030030 cell projection organization IEA --
GO:0032880 regulation of protein localization IEA --
genes like me logo Genes that share ontologies with B9D1: view

No data available for SIGNOR curated interactions for B9D1 Gene

Drugs & Compounds for B9D1 Gene

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  1. Drug
No Compound Related Data Available

Transcripts for B9D1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for B9D1 Gene

(13) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(84) Selected AceView cDNA sequences:
(15) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for B9D1 Gene

B9 protein domain 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for B9D1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c ^ 9
SP1: - - -
SP2: - - - -
SP3: -
SP4: - -
SP5:
SP6: - - - - - -

Relevant External Links for B9D1 Gene

GeneLoc Exon Structure for
B9D1
ECgene alternative splicing isoforms for
B9D1

Expression for B9D1 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for B9D1 Gene

mRNA expression in normal human tissues for B9D1 Gene
mRNA expression by GTEx for B9D1 GenemRNA expression by BioGPS for B9D1 Gene

NURSA nuclear receptor signaling pathways regulating expression of B9D1 Gene:

B9D1

SOURCE GeneReport for Unigene cluster for B9D1 Gene:

Hs.462445

Evidence on tissue expression from TISSUES for B9D1 Gene

  • Skin(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for B9D1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • endocrine
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Organs:
Head and neck:
  • brain
  • cerebellum
  • cerebrospinal fluid
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • meninges
  • mouth
  • neck
  • nose
  • olfactory bulb
  • outer ear
  • skull
  • tongue
  • tooth
Thorax:
  • aorta
  • clavicle
  • diaphragm
  • esophagus
  • heart
  • heart valve
  • lung
Abdomen:
  • abdominal wall
  • adrenal gland
  • biliary tract
  • duodenum
  • intestine
  • kidney
  • large intestine
  • liver
  • pancreas
  • small intestine
  • spleen
  • stomach
Pelvis:
  • anus
  • pelvis
  • penis
  • placenta
  • rectum
  • testicle
  • ureter
  • urethra
  • urinary bladder
  • uterus
  • vagina
  • vulva
Limb:
  • ankle
  • arm
  • digit
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • humerus
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
General:
  • blood
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with B9D1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for B9D1 Gene

Orthologs for B9D1 Gene

This gene was present in the common ancestor of animals.

Orthologs for B9D1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia B9D1 33 34
  • 99.84 (n)
dog
(Canis familiaris)
 Mammalia B9D1 33 34
  • 91.5 (n)
cow
(Bos Taurus)
 Mammalia B9D1 33 34
  • 89.54 (n)
mouse
(Mus musculus)
 Mammalia B9d1 33 16 34
  • 87.91 (n)
rat
(Rattus norvegicus)
 Mammalia LOC100911746 33
  • 87.58 (n)
oppossum
(Monodelphis domestica)
 Mammalia B9D1 34
  • 82 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia B9D1 34
  • 76 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves B9D1 33 34
  • 74.21 (n)
lizard
(Anolis carolinensis)
 Reptilia B9D1 34
  • 68 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia b9d1 33
  • 76.52 (n)
Str.18 33
African clawed frog
(Xenopus laevis)
 Amphibia Xl.23494 33
zebrafish
(Danio rerio)
 Actinopterygii b9d1 33 34
  • 73.23 (n)
fruit fly
(Drosophila melanogaster)
 Insecta CG14870 33 34
  • 49.27 (n)
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP006071 33
  • 48.25 (n)
worm
(Caenorhabditis elegans)
 Secernentea mksr-1 33 34
  • 43.78 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 63 (a)
 OneToOne
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.5634 33
Species where no ortholog for B9D1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for B9D1 Gene

ENSEMBL:
Gene Tree for B9D1 (if available)
TreeFam:
Gene Tree for B9D1 (if available)

Paralogs for B9D1 Gene

Paralogs for B9D1 Gene

genes like me logo Genes that share paralogs with B9D1: view

Variants for B9D1 Gene

Sequence variations from dbSNP and Humsavar for B9D1 Gene

SNP ID Clin Chr 17 pos Variation AA Info Type
rs117169107 likely-benign, Meckel-Gruber syndrome 19,362,679(-) C/T 5_prime_UTR_variant, coding_sequence_variant, intron_variant, missense_variant
rs143149764 conflicting-interpretations-of-pathogenicity, likely-pathogenic, Meckel syndrome, type 9, not provided 19,347,782(-) A/G splice_donor_variant
rs200124070 uncertain-significance, Meckel-Gruber syndrome 19,343,272(-) G/A/C 3_prime_UTR_variant, genic_downstream_transcript_variant, intron_variant
rs201299216 conflicting-interpretations-of-pathogenicity, uncertain-significance, not specified, Meckel-Gruber syndrome, Joubert syndrome 19,347,297(-) A/T coding_sequence_variant, missense_variant
rs2296978 likely-benign, benign, Meckel-Gruber syndrome, not specified 19,362,639(-) C/T 5_prime_UTR_variant, coding_sequence_variant, intron_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for B9D1 Gene

Variant ID Type Subtype PubMed ID
esv3582561 CNV loss 25503493
nsv1061317 CNV gain 25217958
nsv1070395 CNV deletion 25765185
nsv1123099 CNV deletion 24896259
nsv833393 CNV gain+loss 17160897
nsv953845 CNV deletion 24416366

Variation tolerance for B9D1 Gene

Residual Variation Intolerance Score: 42.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 9.65; 89.15% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for B9D1 Gene

Human Gene Mutation Database (HGMD)
B9D1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
B9D1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for B9D1 Gene

Disorders for B9D1 Gene

MalaCards: The human disease database

(6) MalaCards diseases for B9D1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search B9D1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

B9D1_HUMAN
  • 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. {ECO:0000269 PubMed:24886560}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • 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. {ECO:0000269 PubMed:21493627}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for B9D1

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with B9D1: view

No data available for Genatlas for B9D1 Gene

Publications for B9D1 Gene

  1. B9D1 is revealed as a novel Meckel syndrome (MKS) gene by targeted exon-enriched next-generation sequencing and deletion analysis. (PMID: 21493627) Hopp K … Harris PC (Human molecular genetics 2011) 2 3 4 58
  2. Mutations in B9D1 and MKS1 cause mild Joubert syndrome: expanding the genetic overlap with the lethal ciliopathy Meckel syndrome. (PMID: 24886560) Romani M … Valente EM (Orphanet journal of rare diseases 2014) 3 4 58
  3. Functional interactions between the ciliopathy-associated Meckel syndrome 1 (MKS1) protein and two novel MKS1-related (MKSR) proteins. (PMID: 19208769) Bialas NJ … Leroux MR (Journal of cell science 2009) 3 4 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. (PMID: 27173435) Boldt K … UK10K Rare Diseases Group (Nature communications 2016) 3 58

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Sources for B9D1 Gene

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