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HEATR3 HEAT repeat containing 3 [ Homo sapiens (human) ]

Gene ID: 55027, updated on 5-Mar-2024

Summary

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Official Symbol
HEATR3provided by HGNC
Official Full Name
HEAT repeat containing 3provided by HGNC
Primary source
HGNC:HGNC:26087
See related
Ensembl:ENSG00000155393 MIM:614951; AllianceGenome:HGNC:26087
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
SYO1; DBA21
Summary
The protein encoded by this gene plays a role in ribosomal protein transport and in the assembly of the 5S ribonucleoprotein particle (5S RNP). The encoded protein also may be involved in NOD2-mediated NF-kappaB signaling. [provided by RefSeq, Jul 2016]
Expression
Ubiquitous expression in appendix (RPKM 5.5), spleen (RPKM 4.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
16q12.1
Exon count:
17
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (50065970..50107272)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (55863712..55905022)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (50099881..50141183)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene regulation of nuclear pre-mRNA domain containing 1A pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50080479-50080979 Neighboring gene HEATR3 antisense RNA 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:50094586-50094761 Neighboring gene actin gamma 1 pseudogene 16 Neighboring gene Sharpr-MPRA regulatory region 4020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7469 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7468 Neighboring gene MPRA-validated peak2588 silencer Neighboring gene RNY4 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7470 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7471 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:50157041-50157541 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:50177493-50177653 Neighboring gene uncharacterized LOC124900375 Neighboring gene ribosomal protein L10 pseudogene 14

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. HEATR3 variants impair nuclear import of uL18 (RPL5) and drive Diamond-Blackfan anemia. O'Donohue MF, et al. Blood, 2022 May 26. PMID 35213692, Free PMC Article
  2. Genetic variants at 6p21, 10q23, 16q21 and 22q12 are associated with esophageal cancer risk in a Chinese Han population. Jia X, et al. Int J Clin Exp Med, 2015. PMID 26770579, Free PMC Article
  3. Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA-binding site. Calviño FR, et al. Nat Commun, 2015 Apr 7. PMID 25849277, Free PMC Article
  4. Extended haplotype association study in Crohn's disease identifies a novel, Ashkenazi Jewish-specific missense mutation in the NF-κB pathway gene, HEATR3. Zhang W, et al. Genes Immun, 2013 Jul-Aug. PMID 23615072, Free PMC Article
  5. Genome-wide association analyses of esophageal squamous cell carcinoma in Chinese identify multiple susceptibility loci and gene-environment interactions. Wu C, et al. Nat Genet, 2012 Oct. PMID 22960999

See all (46) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. HEATR3 involved in the cell proliferation, metastasis and cell cycle development of bladder cancer acts as a tumor suppressor.
    Title: HEATR3 involved in the cell proliferation, metastasis and cell cycle development of bladder cancer acts as a tumor suppressor.
  2. HEATR3 variants impair nuclear import of uL18 (RPL5) and drive Diamond-Blackfan anemia.
    Title: HEATR3 variants impair nuclear import of uL18 (RPL5) and drive Diamond-Blackfan anemia.
  3. Data indicate that HEATR3 plays a positive role in NOD2-mediated NF-kappaB signaling.
    Title: Extended haplotype association study in Crohn's disease identifies a novel, Ashkenazi Jewish-specific missense mutation in the NF-κB pathway gene, HEATR3.
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
Diamond-Blackfan anemia 21
MedGen: C5774230 OMIM: 620072 GeneReviews: Not available
not available

EBI GWAS Catalog

Description
Genome-wide association analyses of esophageal squamous cell carcinoma in Chinese identify multiple susceptibility loci and gene-environment interactions.
EBI GWAS Catalog
Identification of nine new susceptibility loci for testicular cancer, including variants near DAZL and PRDM14.
EBI GWAS Catalog
Meta-analysis identifies four new loci associated with testicular germ cell tumor.
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

  • FLJ20718

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables unfolded protein binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in erythrocyte maturation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein import into nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein import into nucleus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in ribosomal large subunit biogenesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ribosomal large subunit biogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
HEAT repeat-containing protein 3
Names
symportin 1

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_001329729.2 → NP_001316658.1  HEAT repeat-containing protein 3 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), as well as variant 3, encodes isoform b.
    Source sequence(s)
    AC007610
    UniProtKB/TrEMBL
    A0A8I5KR70
    Conserved Domains (1) summary
    cd13394
    Location:1 → 556
    Syo1_like; Fungal symportin 1 (syo1) and similar proteins

  2. NM_001329730.2 → NP_001316659.1  HEAT repeat-containing protein 3 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3), as well as variant 2, encodes isoform b.
    Source sequence(s)
    AC007610
    UniProtKB/TrEMBL
    A0A8I5KR70
    Conserved Domains (1) summary
    cd13394
    Location:1 → 556
    Syo1_like; Fungal symportin 1 (syo1) and similar proteins

  3. NM_001329731.2 → NP_001316660.1  HEAT repeat-containing protein 3 isoform c

    Status: REVIEWED

    Source sequence(s)
    AC007610
    Conserved Domains (1) summary
    cd13394
    Location:134 → 442
    Syo1_like; Fungal symportin 1 (syo1) and similar proteins

  4. NM_182922.4 → NP_891552.1  HEAT repeat-containing protein 3 isoform a

    See identical proteins and their annotated locations for NP_891552.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AC007610
    Consensus CDS
    CCDS10739.1
    UniProtKB/Swiss-Prot
    A8K1N4, Q7Z4Q2, Q8N525, Q8WV56, Q96CC9, Q9NWN7
    Related
    ENSP00000299192.7, ENST00000299192.8
    Conserved Domains (2) summary
    cd13394
    Location:2 → 673
    Syo1_like; Fungal symportin 1 (syo1) and similar proteins
    sd00043
    Location:69 → 108
    ARM; armadillo repeat [structural motif]

RNA

  1. NR_138092.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC007610

  2. NR_138093.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC007610

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_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    50065970..50107272
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    55863712..55905022
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_017939.1: Suppressed sequence

    Description
    NM_017939.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q7Z4Q2.2 GenPept UniProtKB/Swiss-Prot:Q7Z4Q2

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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