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NBPF3 NBPF member 3 [ Homo sapiens (human) ]

Gene ID: 84224, updated on 5-Mar-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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Location:
1p36.12
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (21436789..21484900)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (21261023..21308825)
105.20220307 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
  • 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. 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
  5. 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

See all (26) 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_2023_10

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

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