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ELAC2 elaC ribonuclease Z 2 [ Homo sapiens (human) ]

Gene ID: 60528, updated on 11-Apr-2024

Summary

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Official Symbol
ELAC2provided by HGNC
Official Full Name
elaC ribonuclease Z 2provided by HGNC
Primary source
HGNC:HGNC:14198
See related
Ensembl:ENSG00000006744 MIM:605367; AllianceGenome:HGNC:14198
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
ELC2; HPC2; COXPD17
Summary
The protein encoded by this gene has a C-terminal domain with tRNA 3′ processing endoribonuclease activity, which catalyzes the removal of the 3' trailer from precursor tRNAs. The protein also interacts with activated Smad family member 2 (Smad2) and its nuclear partner forkhead box H1 (also known as FAST-1), and reduced expression can suppress transforming growth factor-beta induced growth arrest. Mutations in this gene result in an increased risk of prostate cancer. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
Expression
Ubiquitous expression in colon (RPKM 15.0), testis (RPKM 14.9) and 25 other tissues See more
Orthologs
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Genomic context

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See ELAC2 in Genome Data Viewer
Location:
17p12
Exon count:
25
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (12991612..13018027, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (12899079..12925488, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (12894929..12921344, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene myocardin Neighboring gene ARHGAP44 and MYOCD antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8206 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11737 Neighboring gene Rho GTPase activating protein 44 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11739 Neighboring gene microRNA 1269b Neighboring gene Sharpr-MPRA regulatory region 8598 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:12920660-12921160 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8207 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:12999283-13000482 Neighboring gene VISTA enhancer hs1497 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr17:13044042-13044662 Neighboring gene uncharacterized LOC124904097 Neighboring gene long intergenic non-protein coding RNA 2093

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. A Study of Ser217Leu and Ala541Thr Polymorphism in the Men Afflicted with Prostate Cancer and in the Men being Suspicious of Prostate Cancer. Zahiri Z, et al. Asian Pac J Cancer Prev, 2020 Jun 1. PMID 32592348, Free PMC Article
  2. Mutations in ELAC2 associated with hypertrophic cardiomyopathy impair mitochondrial tRNA 3'-end processing. Saoura M, et al. Hum Mutat, 2019 Oct. PMID 31045291, Free PMC Article
  3. The Phenotype and Outcome of Infantile Cardiomyopathy Caused by a Homozygous ELAC2 Mutation. Shinwari ZMA, et al. Cardiology, 2017. PMID 28441660
  4. A homozygous splicing mutation in ELAC2 suggests phenotypic variability including intellectual disability with minimal cardiac involvement. Akawi NA, et al. Orphanet J Rare Dis, 2016 Oct 21. PMID 27769300, Free PMC Article
  5. ELAC2 polymorphisms and prostate cancer risk: a meta-analysis based on 18 case-control studies. Xu B, et al. Prostate Cancer Prostatic Dis, 2010 Sep. PMID 20231859, Free PMC Article

See all (105) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. ELAC2 is a functional prostate cancer risk allele.
    Title: ELAC2 is a functional prostate cancer risk allele.
  2. A Study of Ser217Leu and Ala541Thr Polymorphism in the Men Afflicted with Prostate Cancer and in the Men being Suspicious of Prostate Cancer.
    Title: A Study of Ser217Leu and Ala541Thr Polymorphism in the Men Afflicted with Prostate Cancer and in the Men being Suspicious of Prostate Cancer.
  3. Our study thus broadly confirms the correlation of ELAC2 variants with severe infantile-onset forms of HCM and mitochondrial respiratory chain dysfunction.
    Title: Mutations in ELAC2 associated with hypertrophic cardiomyopathy impair mitochondrial tRNA 3'-end processing.
  4. This study describes the cardiac phenotype and outcome of ELAC2 mutation in Infantile Cardiomyopathy
    Title: The Phenotype and Outcome of Infantile Cardiomyopathy Caused by a Homozygous ELAC2 Mutation.
  5. ELAC2 rs11545302 polymorphism was associated with PSA > 20 and rs4792311 was associated with TNM > 2.
    Title: Association between RNASEL, MSR1, and ELAC2 single nucleotide polymorphisms and gene expression in prostate cancer risk.
  6. A homozygous splicing mutation in ELAC2 suggests phenotypic variability including intellectual disability with minimal cardiac involvement
    Title: A homozygous splicing mutation in ELAC2 suggests phenotypic variability including intellectual disability with minimal cardiac involvement.
  7. ELAC2 mutations cause a mitochondrial RNA processing defect associated with hypertrophic cardiomyopathy.
    Title: ELAC2 mutations cause a mitochondrial RNA processing defect associated with hypertrophic cardiomyopathy.
  8. results indicate that ELAC2 functions as a tRNase Z in human mitochondria and suggest that mt-tRNase Z preferentially cleaves molecules already processed by the proteinaceous mtRNase P
    Title: Involvement of human ELAC2 gene product in 3' end processing of mitochondrial tRNAs.
  9. ELAC2 and PTCD1 affect the 3' end processing of tRNAs.
    Title: RNA processing in human mitochondria.
  10. analysis of dual nuclear/mitochondrial targeting of the ELAC2 gene product by alternative translation initiation
    Title: Localization of human RNase Z isoforms: dual nuclear/mitochondrial targeting of the ELAC2 gene product by alternative translation initiation.
Submit: New GeneRIF Correction See all GeneRIFs (40)

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
Combined oxidative phosphorylation defect type 17
MedGen: C3809526 OMIM: 615440 GeneReviews: Not available
Compare labs
Prostate cancer, hereditary, 2
MedGen: C3539120 OMIM: 614731 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)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10530, FLJ36693, FLJ42848

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 3'-tRNA processing endoribonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA binding HDA PubMed 
enables RNA endonuclease activity TAS
Traceable Author Statement
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables tRNA-specific ribonuclease activity EXP
Inferred from Experiment
more info
 PubMed 
Process Evidence Code Pubs
involved_in mitochondrial tRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mitochondrial tRNA 3'-end processing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mitochondrial tRNA processing TAS
Traceable Author Statement
more info
  
involved_in tRNA 3'-end processing TAS
Traceable Author Statement
more info
  
involved_in tRNA decay TAS
Traceable Author Statement
more info
  
Component Evidence Code Pubs
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in mitochondrial matrix TAS
Traceable Author Statement
more info
  
located_in mitochondrial nucleoid IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in mitochondrion IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in mitochondrion IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
zinc phosphodiesterase ELAC protein 2
Names
RNase Z 2
elaC homolog 2
elaC homolog protein 2
elaC-like protein 2
heredity prostate cancer protein 2
putative prostate cancer susceptibility protein HPC2/ELAC2
ribonuclease Z 2
tRNA 3 endonuclease 2
tRNase Z (long form)
tRNase Z 2
NP_001159434.1
NP_060597.4
NP_776065.1
XP_024306628.1
XP_024306629.1
XP_054172839.1
XP_054172840.1

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.

Genomic

  1. NG_015808.1 RefSeqGene

    Range
    5038..31453
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001165962.2 → NP_001159434.1  zinc phosphodiesterase ELAC protein 2 isoform 3

    See identical proteins and their annotated locations for NP_001159434.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region, compared to variant 1. The resulting isoform (3) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AA706335, AC005277, AK298397, DC394013
    Consensus CDS
    CCDS54093.1
    UniProtKB/TrEMBL
    B4DT15
    Related
    ENSP00000405223.3, ENST00000426905.7
    Conserved Domains (4) summary
    COG1234
    Location:442 → 712
    ElaC; Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis]
    cd07718
    Location:443 → 648
    RNaseZ_ELAC1_ELAC2-C-term-like_MBL-fold; Ribonuclease Z ELAC1, C-terminus of ELAC2, and related proteins; MBL-fold metallo-hydrolase domain
    cd16296
    Location:60 → 271
    RNaseZ_ELAC2-N-term-like_MBL-fold; Ribonuclease Z, N-terminus of human ELAC2 and related proteins; MBL-fold metallo-hydrolase domain
    cl23716
    Location:616 → 690
    metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

  2. NM_018127.7 → NP_060597.4  zinc phosphodiesterase ELAC protein 2 isoform 1

    See identical proteins and their annotated locations for NP_060597.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AA706335, AC005277, AF304370, DC394013
    Consensus CDS
    CCDS11164.1
    UniProtKB/Swiss-Prot
    B4DPL9, Q6IA94, Q9BQ52, Q9HAS8, Q9HAS9, Q9NVT1
    UniProtKB/TrEMBL
    A0A0S2Z5M8, B4DT15
    Related
    ENSP00000337445.4, ENST00000338034.9
    Conserved Domains (4) summary
    COG1234
    Location:482 → 752
    ElaC; Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis]
    cd07718
    Location:483 → 688
    RNaseZ_ELAC1_ELAC2-C-term-like_MBL-fold; Ribonuclease Z ELAC1, C-terminus of ELAC2, and related proteins; MBL-fold metallo-hydrolase domain
    cd16296
    Location:60 → 311
    RNaseZ_ELAC2-N-term-like_MBL-fold; Ribonuclease Z, N-terminus of human ELAC2 and related proteins; MBL-fold metallo-hydrolase domain
    cl23716
    Location:656 → 730
    metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

  3. NM_173717.2 → NP_776065.1  zinc phosphodiesterase ELAC protein 2 isoform 2

    See identical proteins and their annotated locations for NP_776065.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region. The resulting isoform (2) lacks one amino acid, compared to isoform 1.
    Source sequence(s)
    AA706335, AC005277, AK001392, BC001939, DC394013
    UniProtKB/TrEMBL
    B4DT15
    Conserved Domains (4) summary
    COG1234
    Location:481 → 751
    ElaC; Ribonuclease BN, tRNA processing enzyme [Translation, ribosomal structure and biogenesis]
    cd07718
    Location:482 → 687
    RNaseZ_ELAC1_ELAC2-C-term-like_MBL-fold; Ribonuclease Z ELAC1, C-terminus of ELAC2, and related proteins; MBL-fold metallo-hydrolase domain
    cd16296
    Location:60 → 311
    RNaseZ_ELAC2-N-term-like_MBL-fold; Ribonuclease Z, N-terminus of human ELAC2 and related proteins; MBL-fold metallo-hydrolase domain
    cl23716
    Location:655 → 729
    metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    12991612..13018027 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024450861.2 → XP_024306629.1  zinc phosphodiesterase ELAC protein 2 isoform X1

    UniProtKB/TrEMBL
    G5E9D5
    Related
    ENSP00000463740.2, ENST00000584650.5
    Conserved Domains (2) summary
    cd07718
    Location:389 → 594
    RNaseZ_ELAC1_ELAC2-C-term-like_MBL-fold; Ribonuclease Z ELAC1, C-terminus of ELAC2, and related proteins; MBL-fold metallo-hydrolase domain
    cl23716
    Location:1 → 217
    metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

  2. XM_024450860.2 → XP_024306628.1  zinc phosphodiesterase ELAC protein 2 isoform X1

    UniProtKB/TrEMBL
    G5E9D5
    Conserved Domains (2) summary
    cd07718
    Location:389 → 594
    RNaseZ_ELAC1_ELAC2-C-term-like_MBL-fold; Ribonuclease Z ELAC1, C-terminus of ELAC2, and related proteins; MBL-fold metallo-hydrolase domain
    cl23716
    Location:1 → 217
    metallo-hydrolase-like_MBL-fold; mainly hydrolytic enzymes and related proteins which carry out various biological functions; MBL-fold metallohydrolase domain

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    12899079..12925488 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054316864.1 → XP_054172839.1  zinc phosphodiesterase ELAC protein 2 isoform X1

  2. XM_054316865.1 → XP_054172840.1  zinc phosphodiesterase ELAC protein 2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BQ52.2 GenPept UniProtKB/Swiss-Prot:Q9BQ52

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