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    VWA3B von Willebrand factor A domain containing 3B [ Homo sapiens (human) ]

    Gene ID: 200403, updated on 2-Nov-2024

    Summary

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    Official Symbol
    VWA3Bprovided by HGNC
    Official Full Name
    von Willebrand factor A domain containing 3Bprovided by HGNC
    Primary source
    HGNC:HGNC:28385
    See related
    Ensembl:ENSG00000168658 MIM:614884; AllianceGenome:HGNC:28385
    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
    SCAR22
    Summary
    This gene encodes an intracellular protein that contains a von Willebrand factor type A domain. Intracellular proteins with VWA domains are thought to function in transcription, DNA repair, ribosomal and membrane transport and the proteasome. Mutations in this gene are associated with Spinocerebellar ataxia, autosomal recessive 22. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, May 2017]
    Expression
    Restricted expression toward testis (RPKM 15.5) See more
    Orthologs
    mouse all
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    Genomic context

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    See VWA3B in Genome Data Viewer
    Location:
    2q11.2
    Exon count:
    37
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (98087167..98330616)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (98545383..98788821)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (98703630..98929762)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124905591 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16252 Neighboring gene MIR2 retrotransposon enhancer-blocking element Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11797 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11798 Neighboring gene uncharacterized LOC105373501 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:98663772-98664272 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:98664273-98664773 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:98670618-98671817 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98703358-98703858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98703859-98704359 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98733463-98733964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98733965-98734464 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11799 Neighboring gene Sharpr-MPRA regulatory region 9320 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:98746447-98747273 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:98748232-98748818 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:98748819-98749404 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:98750133-98751332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98779443-98779989 Neighboring gene NANOG hESC enhancer GRCh37_chr2:98808643-98809198 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:98810042-98810239 Neighboring gene ATP synthase F1 subunit beta pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98896664-98897164 Neighboring gene NANOG hESC enhancer GRCh37_chr2:98933593-98934329 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:98950857-98951787 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:98963419-98963930 Neighboring gene Sharpr-MPRA regulatory region 13649 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98993983-98994750 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:98998693-98999270 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr2:98999847-99000424 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:99000425-99001000 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:99004561-99004748 Neighboring gene cyclic nucleotide gated channel subunit alpha 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16257 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:99051832-99053031 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16258 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16259 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16260 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:99079757-99080272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16261 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:99082317-99082881 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16265 Neighboring gene inositol polyphosphate-4-phosphatase type I A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16267 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:99136086-99136586 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:99136587-99137087 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16268 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:99170837-99171337 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:99176784-99176955 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:99190711-99190893 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:99200423-99200924 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:99209219-99209372

    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 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. A homozygous mutation of VWA3B causes cerebellar ataxia with intellectual disability. Kawarai T, et al. J Neurol Neurosurg Psychiatry, 2016 Jun. PMID 26157035
    2. Non-EST-based prediction of novel alternatively spliced cassette exons with cell signaling function in Caenorhabditis elegans and human. Leparc GG, et al. Nucleic Acids Res, 2007. PMID 17452356, Free PMC Article
    3. Hereditary Ataxia Overview. Adam MP, et al. , 1993. PMID 20301317
    4. Protein interaction landscapes revealed by advanced in vivo cross-linking-mass spectrometry. Wheat A, et al. Proc Natl Acad Sci U S A, 2021 Aug 10. PMID 34349018, Free PMC Article
    5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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
    Spinocerebellar ataxia, autosomal recessive 22
    MedGen: C4310781 OMIM: 616948 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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ32686, MGC26733

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    von Willebrand factor A domain-containing protein 3B
    Names
    VWA domain-containing protein 3B

    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_054753.1 RefSeqGene

      Range
      5036..231168
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001345864.2 → NP_001332793.1  von Willebrand factor A domain-containing protein 3B isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AC092675, AC112788, AK295743, AL834385
      UniProtKB/TrEMBL
      B7Z3D8

    2. NM_144992.5 → NP_659429.4  von Willebrand factor A domain-containing protein 3B isoform 1

      See identical proteins and their annotated locations for NP_659429.4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC018691, AC092675, AL834385, BC095480, DB090320
      Consensus CDS
      CCDS42718.1
      UniProtKB/Swiss-Prot
      B9EK71, Q502W6, Q86T73, Q8N2D0, Q8N770, Q8NA79, Q8ND63, Q8ND65, Q8WW02
      Related
      ENSP00000417955.1, ENST00000477737.6
      Conserved Domains (3) summary
      cd00198
      Location:508 → 659
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      pfam15057
      Location:1037 → 1161
      DUF4537; Domain of unknown function (DUF4537)
      cl00057
      Location:142 → 293
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    RNA

    1. NR_144296.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains two alternate exons and lacks another alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC018691, AC092675, AC112788, AL832761
      Related
      ENST00000432242.5

    2. NR_144297.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate exon, contains another alternate exon, and differs in the 3' end compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC018691, BC026091, BI463112
      Related
      ENST00000416277.5

    3. NR_144298.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks three alternate exons and differs in the 3' end compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC018691, AK057248, BI463112
      Related
      ENST00000448638.5

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      98087167..98330616
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011510772.2 → XP_011509074.1  von Willebrand factor A domain-containing protein 3B isoform X4

      Conserved Domains (3) summary
      cd00198
      Location:508 → 659
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      cl00057
      Location:142 → 293
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      cl02573
      Location:1037 → 1115
      TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

    2. XM_011510770.2 → XP_011509072.1  von Willebrand factor A domain-containing protein 3B isoform X2

      Conserved Domains (3) summary
      cd00198
      Location:508 → 659
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      pfam15057
      Location:1020 → 1144
      DUF4537; Domain of unknown function (DUF4537)
      cl00057
      Location:142 → 293
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    3. XM_005263897.3 → XP_005263954.1  von Willebrand factor A domain-containing protein 3B isoform X1

      UniProtKB/Swiss-Prot
      Q502W6
      Conserved Domains (3) summary
      cd00198
      Location:508 → 659
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      pfam15057
      Location:1037 → 1161
      DUF4537; Domain of unknown function (DUF4537)
      cl00057
      Location:142 → 293
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    4. XM_011510771.3 → XP_011509073.1  von Willebrand factor A domain-containing protein 3B isoform X3

      Conserved Domains (3) summary
      cd00198
      Location:466 → 617
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      pfam15057
      Location:995 → 1119
      DUF4537; Domain of unknown function (DUF4537)
      cl00057
      Location:142 → 293
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    5. XM_017003564.2 → XP_016859053.1  von Willebrand factor A domain-containing protein 3B isoform X7

    6. XM_011510774.1 → XP_011509076.1  von Willebrand factor A domain-containing protein 3B isoform X8

      Conserved Domains (2) summary
      cd00198
      Location:508 → 659
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      cl00057
      Location:142 → 293
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    7. XM_047443648.1 → XP_047299604.1  von Willebrand factor A domain-containing protein 3B isoform X12

      Related
      ENSP00000388158.1, ENST00000433678.5

    8. XM_011510775.3 → XP_011509077.1  von Willebrand factor A domain-containing protein 3B isoform X11

      Conserved Domains (2) summary
      cd00198
      Location:508 → 612
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      cl00057
      Location:142 → 293
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

    9. XM_047443640.1 → XP_047299596.1  von Willebrand factor A domain-containing protein 3B isoform X5

    10. XM_047443641.1 → XP_047299597.1  von Willebrand factor A domain-containing protein 3B isoform X6

    11. XM_017003561.2 → XP_016859050.1  von Willebrand factor A domain-containing protein 3B isoform X6

      UniProtKB/TrEMBL
      B7Z3D8
      Conserved Domains (2) summary
      cd00198
      Location:165 → 316
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      pfam15057
      Location:694 → 818
      DUF4537; Domain of unknown function (DUF4537)

    12. XM_017003562.2 → XP_016859051.1  von Willebrand factor A domain-containing protein 3B isoform X6

      UniProtKB/TrEMBL
      B7Z3D8
      Conserved Domains (2) summary
      cd00198
      Location:165 → 316
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      pfam15057
      Location:694 → 818
      DUF4537; Domain of unknown function (DUF4537)

    13. XM_006712359.4 → XP_006712422.1  von Willebrand factor A domain-containing protein 3B isoform X9

      UniProtKB/TrEMBL
      H0YEM4
      Conserved Domains (2) summary
      cd00198
      Location:27 → 178
      vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...
      pfam15057
      Location:556 → 680
      DUF4537; Domain of unknown function (DUF4537)

    14. XM_047443645.1 → XP_047299601.1  von Willebrand factor A domain-containing protein 3B isoform X10

      Related
      ENSP00000436153.1, ENST00000473149.5

    RNA

    1. XR_922885.4 RNA Sequence

    2. XR_922884.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      98545383..98788821
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054340936.1 → XP_054196911.1  von Willebrand factor A domain-containing protein 3B isoform X4

    2. XM_054340934.1 → XP_054196909.1  von Willebrand factor A domain-containing protein 3B isoform X2

    3. XM_054340933.1 → XP_054196908.1  von Willebrand factor A domain-containing protein 3B isoform X1

    4. XM_054340935.1 → XP_054196910.1  von Willebrand factor A domain-containing protein 3B isoform X3

    5. XM_054340941.1 → XP_054196916.1  von Willebrand factor A domain-containing protein 3B isoform X7

    6. XM_054340942.1 → XP_054196917.1  von Willebrand factor A domain-containing protein 3B isoform X8

    7. XM_054340946.1 → XP_054196921.1  von Willebrand factor A domain-containing protein 3B isoform X12

    8. XM_054340945.1 → XP_054196920.1  von Willebrand factor A domain-containing protein 3B isoform X11

    9. XM_054340937.1 → XP_054196912.1  von Willebrand factor A domain-containing protein 3B isoform X5

    10. XM_054340939.1 → XP_054196914.1  von Willebrand factor A domain-containing protein 3B isoform X6

    11. XM_054340938.1 → XP_054196913.1  von Willebrand factor A domain-containing protein 3B isoform X6

    12. XM_054340940.1 → XP_054196915.1  von Willebrand factor A domain-containing protein 3B isoform X6

    13. XM_054340943.1 → XP_054196918.1  von Willebrand factor A domain-containing protein 3B isoform X9

    14. XM_054340944.1 → XP_054196919.1  von Willebrand factor A domain-containing protein 3B isoform X10

    RNA

    1. XR_008486303.1 RNA Sequence

    2. XR_008486302.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q502W6.3 GenPept UniProtKB/Swiss-Prot:Q502W6

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