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    NBPF3 NBPF member 3 [ Homo sapiens (human) ]

    Gene ID: 84224, updated on 2-Nov-2024

    Summary

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    Official Symbol
    NBPF3provided by HGNC
    Official Full Name
    NBPF member 3provided by HGNC
    Primary source
    HGNC:HGNC:25076
    See related
    Ensembl:ENSG00000142794 MIM:612992; AllianceGenome:HGNC:25076
    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
    AE2
    Summary
    This gene is a member of the neuroblastoma breakpoint family (NBPF) which consists of dozens of recently duplicated genes primarily located in segmental duplications on human chromosome 1. This gene family has experienced its greatest expansion within the human lineage and has expanded, to a lesser extent, among primates in general. Members of this gene family are characterized by tandemly repeated copies of DUF1220 protein domains. DUF1220 copy number variations in human chromosomal region 1q21.1, where most DUF1220 domains are located, have been implicated in a number of developmental and neurogenetic diseases such as microcephaly, macrocephaly, autism, schizophrenia, cognitive disability, congenital heart disease, neuroblastoma, and congenital kidney and urinary tract anomalies. Altered expression of some gene family members is associated with several types of cancer. This gene family contains numerous pseudogenes. [provided by RefSeq, Feb 2013]
    Expression
    Broad expression in testis (RPKM 10.2), thyroid (RPKM 3.5) and 23 other tissues See more
    Orthologs
    all
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    Genomic context

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    See NBPF3 in Genome Data Viewer
    Location:
    1p36.12
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (21436789..21484900)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (21261023..21308825)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (21766630..21811393)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21754875-21755394 Neighboring gene Sharpr-MPRA regulatory region 1847 Neighboring gene NBPF member 2, pseudogene Neighboring gene heparan sulfate 6-O-sulfotransferase 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 381 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21766764-21767274 Neighboring gene Sharpr-MPRA regulatory region 4165 Neighboring gene CROCC pseudogene 5 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:21791822-21793021 Neighboring gene profilin 1 pseudogene 10 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21817787-21818287 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 383 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21835859-21836429 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21836430-21836999 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 334 Neighboring gene alkaline phosphatase, biomineralization associated Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:21860784-21861513 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21863949-21864466 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21864467-21864985 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21895010-21895594 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21900641-21901315 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:21901316-21901990 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21904065-21904588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:21917321-21917860 Neighboring gene long intergenic non-protein coding RNA 2596

    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. Decreased serum pyridoxal levels in schizophrenia: meta-analysis and Mendelian randomization analysis. Tomioka Y, et al. J Psychiatry Neurosci, 2018 May. PMID 29688875, Free PMC Article
    2. Insertion of an HERV(K) LTR in the intron of NBPF3 is not required for its transcriptional activity. Vandepoele K, et al. Virology, 2007 May 25. PMID 17391723
    3. Anion exchanger 2 (AE2) binds to erythrocyte ankyrin and is colocalized with ankyrin along the basolateral plasma membrane of human gastric parietal cells. Jöns T, et al. Eur J Cell Biol, 1998 Mar. PMID 9587054
    4. Genome-wide association study of vitamin B6, vitamin B12, folate, and homocysteine blood concentrations. Tanaka T, et al. Am J Hum Genet, 2009 Apr. PMID 19303062, Free PMC Article
    5. Genetic Associations with Plasma B12, B6, and Folate Levels in an Ischemic Stroke Population from the Vitamin Intervention for Stroke Prevention (VISP) Trial. Keene KL, et al. Front Public Health, 2014. PMID 25147783, Free PMC Article

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. failed to find a significant association between nbpf3 and schizophrenia.
      Title: Decreased serum pyridoxal levels in schizophrenia: meta-analysis and Mendelian randomization analysis.
    2. Study shows that an NBPF gene lacking this insertion, NBPF3, is expressed in a variety of tissues; thus the effect of HERV(K) LTR insertion on NBPF gene expression remains unknown.
      Title: Insertion of an HERV(K) LTR in the intron of NBPF3 is not required for its transcriptional activity.
    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

    EBI GWAS Catalog

    Description
    Common genetic variants associate with serum phosphorus concentration.
    EBI GWAS Catalog
    Genetic Associations with Plasma B12, B6, and Folate Levels in an Ischemic Stroke Population from the Vitamin Intervention for Stroke Prevention (VISP) Trial.
    EBI GWAS Catalog
    Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.
    EBI GWAS Catalog
    Genome-wide association study of vitamin B6, vitamin B12, folate, and homocysteine blood concentrations.
    EBI GWAS Catalog
    Genome-wide significant predictors of metabolites in the one-carbon metabolism pathway.
    EBI GWAS Catalog
    Population-based genome-wide association studies reveal six loci influencing plasma levels of liver enzymes.
    EBI GWAS Catalog

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • DKFZp434D177

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    neuroblastoma breakpoint family member 3
    Names
    protein SHIIIa4

    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.

    mRNA and Protein(s)

    1. NM_001256416.4 → NP_001243345.1  neuroblastoma breakpoint family member 3 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks one exon and includes an alternate exon in the coding region, compared to variant 1. It encodes isoform 2 which is shorter, compared to isoform 1.
      Source sequence(s)
      AK292580, AK314597, AL136890, AL592309, BC024011
      Consensus CDS
      CCDS57976.1
      UniProtKB/Swiss-Prot
      Q9H094
      Related
      ENSP00000340336.5, ENST00000342104.9
      Conserved Domains (1) summary
      pfam06758
      Location:459 → 521
      DUF1220; Repeat of unknown function (DUF1220)

    2. NM_001256417.4 → NP_001243346.1  neuroblastoma breakpoint family member 3 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon in the coding region, compared to variant 1. The resulting protein (isoform 3) is shorter, compared to isoform 1.
      Source sequence(s)
      AK292580, AK299840, AL136890, AL592309
      Consensus CDS
      CCDS57977.1
      UniProtKB/Swiss-Prot
      Q9H094
      Related
      ENSP00000415711.2, ENST00000454000.6
      Conserved Domains (1) summary
      pfam06758
      Location:401 → 463
      DUF1220; Repeat of unknown function (DUF1220)

    3. NM_001330381.3 → NP_001317310.1  neuroblastoma breakpoint family member 3 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) contains several alternate internal exons compared to variant 1. The resulting isoform (4) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AL592309
      Consensus CDS
      CCDS81275.1
      UniProtKB/Swiss-Prot
      Q9H094
      Conserved Domains (1) summary
      pfam06758
      Location:411 → 476
      DUF1220; Repeat of unknown function (DUF1220)

    4. NM_001377491.1 → NP_001364420.1  neuroblastoma breakpoint family member 3 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL592309
      Consensus CDS
      CCDS81275.1
      Related
      ENSP00000484028.1, ENST00000619554.1

    5. NM_001377492.1 → NP_001364421.1  neuroblastoma breakpoint family member 3 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL592309
      Consensus CDS
      CCDS81275.1

    6. NM_001377493.1 → NP_001364422.1  neuroblastoma breakpoint family member 3 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL592309
      Consensus CDS
      CCDS81275.1

    7. NM_001377494.1 → NP_001364423.1  neuroblastoma breakpoint family member 3 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL592309
      Consensus CDS
      CCDS81275.1

    8. NM_001377495.1 → NP_001364424.1  neuroblastoma breakpoint family member 3 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL592309
      Consensus CDS
      CCDS81275.1

    9. NM_001377496.1 → NP_001364425.1  neuroblastoma breakpoint family member 3 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AL592309
      Conserved Domains (1) summary
      pfam06758
      Location:374 → 439
      DUF1220; Repeat of unknown function (DUF1220)

    10. NM_032264.6 → NP_115640.1  neuroblastoma breakpoint family member 3 isoform 1

      See identical proteins and their annotated locations for NP_115640.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest protein (isoform 1).
      Source sequence(s)
      AL592309
      Consensus CDS
      CCDS216.1
      UniProtKB/Swiss-Prot
      A8K965, B4DSP2, I3L0I8, Q3BBW1, Q5VTG2, Q5VTG3, Q5VTG4, Q8IX78, Q8ND86, Q8TC96, Q9H094
      Related
      ENSP00000316782.5, ENST00000318249.10
      Conserved Domains (1) summary
      pfam06758
      Location:471 → 533
      DUF1220; Repeat of unknown function (DUF1220)

    RNA

    1. NR_046176.4 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains several alternate exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK095602, AK292580, AL136890, AL592309
      Related
      ENST00000318220.10

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      21436789..21484900
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047432037.1 → XP_047287993.1  neuroblastoma breakpoint family member 3 isoform X1

      UniProtKB/Swiss-Prot
      A8K965, B4DSP2, I3L0I8, Q3BBW1, Q5VTG2, Q5VTG3, Q5VTG4, Q8IX78, Q8ND86, Q8TC96, Q9H094

    2. XM_047432038.1 → XP_047287994.1  neuroblastoma breakpoint family member 3 isoform X1

      UniProtKB/Swiss-Prot
      A8K965, B4DSP2, I3L0I8, Q3BBW1, Q5VTG2, Q5VTG3, Q5VTG4, Q8IX78, Q8ND86, Q8TC96, Q9H094

    3. XM_047432039.1 → XP_047287995.1  neuroblastoma breakpoint family member 3 isoform X2

    4. XM_006710957.2 → XP_006711020.1  neuroblastoma breakpoint family member 3 isoform X2

      Conserved Domains (1) summary
      pfam06758
      Location:434 → 496
      DUF1220; Repeat of unknown function (DUF1220)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      21261023..21308825
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339127.1 → XP_054195102.1  neuroblastoma breakpoint family member 3 isoform X1

    2. XM_054339128.1 → XP_054195103.1  neuroblastoma breakpoint family member 3 isoform X1

    3. XM_054339130.1 → XP_054195105.1  neuroblastoma breakpoint family member 3 isoform X2

    4. XM_054339129.1 → XP_054195104.1  neuroblastoma breakpoint family member 3 isoform X2

    5. XM_054339131.1 → XP_054195106.1  neuroblastoma breakpoint family member 3 isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H094.1 GenPept UniProtKB/Swiss-Prot:Q9H094

    Gene LinkOut

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