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    HORMAD2 HORMA domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 150280, updated on 27-Nov-2024

    Summary

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    Official Symbol
    HORMAD2provided by HGNC
    Official Full Name
    HORMA domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:28383
    See related
    Ensembl:ENSG00000176635 MIM:618842; AllianceGenome:HGNC:28383
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CT46.2
    Summary
    Predicted to be involved in meiotic cell cycle and meiotic sister chromatid cohesion. Located in centrosome; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Restricted expression toward testis (RPKM 6.8) See more
    Orthologs
    mouse all
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    Genomic context

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    See HORMAD2 in Genome Data Viewer
    Location:
    22q12.2
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (30077732..30207456)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (30541076..30670783)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (30476453..30573064)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene myotubularin related protein 3 Neighboring gene HORMAD2 and MTMR3 antisense RNA 1 Neighboring gene microRNA 6818 Neighboring gene calponin 2 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13600 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18825 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:30475909-30476606 Neighboring gene ribosomal protein L36 pseudogene 17 Neighboring gene RPS3A pseudogene 51 Neighboring gene uncharacterized LOC105372988 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18827 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:30601719-30602918 Neighboring gene Sharpr-MPRA regulatory region 10236 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:30610529-30611063 Neighboring gene CRISPRi-validated cis-regulatory element chr22.1257 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:30617260-30617890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30618871-30619372 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30619373-30619872 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:30622687-30623483 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:30624775-30625710 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30627593-30628226 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30631328-30631830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30637625-30638293 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:30640698-30641198 Neighboring gene LIF antisense RNA 1 Neighboring gene LIF antisense RNA 2 Neighboring gene LIF interleukin 6 family cytokine

    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 homozygous stop codon in HORMAD2 in a patient with recurrent digynic triploid miscarriage. Liang M, et al. Mol Genet Genomic Med, 2024 Feb. PMID 38400599, Free PMC Article
    2. HORMAD2 methylation-mediated epigenetic regulation of gene expression in thyroid cancer. Lin Q, et al. J Cell Mol Med, 2018 Oct. PMID 30039914, Free PMC Article
    3. HORMAD2/CT46.2, a novel cancer/testis gene, is ectopically expressed in lung cancer tissues. Liu M, et al. Mol Hum Reprod, 2012 Dec. PMID 22893617
    4. Association of polymorphisms at HORMAD2 and prognosis in advanced non-small-cell lung cancer patients. Zhang K, et al. Cancer Epidemiol, 2014 Aug. PMID 24797335
    5. Genome-wide association study identifies variants in HORMAD2 associated with tonsillectomy. Feenstra B, et al. J Med Genet, 2017 May. PMID 27941131

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A homozygous stop codon in HORMAD2 in a patient with recurrent digynic triploid miscarriage.
      Title: A homozygous stop codon in HORMAD2 in a patient with recurrent digynic triploid miscarriage.
    2. Identification of susceptibility locus shared by IgA nephropathy and inflammatory bowel disease in a Chinese Han population.
      Title: Identification of susceptibility locus shared by IgA nephropathy and inflammatory bowel disease in a Chinese Han population.
    3. Hypermethylation of HORMAD2 could induce thyroid carcinoma progression, while hypomethylation of HORMAD2 retards cell growth and mobility and facilitates apoptosis through increasing its mRNA expression.
      Title: HORMAD2 methylation-mediated epigenetic regulation of gene expression in thyroid cancer.
    4. The variant rs2412971, intronic in HORMAD2 at chromosome 22q12.2, was robustly associated with tonsillectomy.
      Title: Genome-wide association study identifies variants in HORMAD2 associated with tonsillectomy.
    5. Hormad1 and Hormad2 might not be the susceptible genes for the non-obstructive azoospermia in our study population. However, rs718772 of Hormad2 variant might be associated with testis development in NOA patients.
      Title: Genetic study of Hormad1 and Hormad2 with non-obstructive azoospermia patients in the male Chinese population.
    6. These findings indicate that polymorphisms at the CT gene HORMAD2 might be involved in the prognosis of advanced non-small-cell lung cancer in Han Chinese.
      Title: Association of polymorphisms at HORMAD2 and prognosis in advanced non-small-cell lung cancer patients.
    7. HORMAD2 is predominantly expressed in human testis and weakly expressed in liver. HORMAD2 is ectopically expressed in nearly 10% of lung cancer samples from Chinese Han individuals.
      Title: HORMAD2/CT46.2, a novel cancer/testis gene, is ectopically expressed in lung cancer tissues.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association between genome-wide association studies reported SNPs and pediatric-onset Crohn's disease in Canadian children.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Common variants at five new loci associated with early-onset inflammatory bowel disease.
    EBI GWAS Catalog
    Genome-wide association study identifies susceptibility loci for IgA nephropathy.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    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)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    integrase gag-pol Analysis of HIV-1 proviral integration sites in antiretroviral treatment patients indicates that HORMAD2 gene favors HIV-1 integration for expansion and persistence of infected cells, suggesting HIV-1 IN interacts with HORMAD2 PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • MGC26710

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in meiotic cell cycle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in meiotic sister chromatid cohesion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    		  
    located_in chromosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in synaptonemal complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    HORMA domain-containing protein 2

    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_001329457.2 → NP_001316386.1  HORMA domain-containing protein 2 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      BC030013, BI829841, HY002382
      Consensus CDS
      CCDS46683.1
      UniProtKB/Swiss-Prot
      B5MEB2, Q8N7B1, Q8NHR2
      Related
      ENSP00000385055.1, ENST00000403975.1
      Conserved Domains (1) summary
      pfam02301
      Location:31 → 228
      HORMA; HORMA domain

    2. NM_001329458.2 → NP_001316387.1  HORMA domain-containing protein 2 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and lacks an alternate exon compared to variant 1. The resulting isoform (b) has a shorter and distinct N-terminus compared to isoform a.
      Source sequence(s)
      BC030013, BI459310, BI829841
      UniProtKB/Swiss-Prot
      Q8N7B1

    3. NM_152510.4 → NP_689723.1  HORMA domain-containing protein 2 isoform a

      See identical proteins and their annotated locations for NP_689723.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      BC030013, BI829841
      Consensus CDS
      CCDS46683.1
      UniProtKB/Swiss-Prot
      B5MEB2, Q8N7B1, Q8NHR2
      Related
      ENSP00000336984.6, ENST00000336726.11
      Conserved Domains (1) summary
      pfam02301
      Location:31 → 228
      HORMA; HORMA domain

    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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      30077732..30207456
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047441154.1 → XP_047297110.1  HORMA domain-containing protein 2 isoform X1

    2. XM_047441156.1 → XP_047297112.1  HORMA domain-containing protein 2 isoform X2

      UniProtKB/Swiss-Prot
      B5MEB2, Q8N7B1, Q8NHR2

    3. XM_047441155.1 → XP_047297111.1  HORMA domain-containing protein 2 isoform X1

    4. XM_017028622.2 → XP_016884111.1  HORMA domain-containing protein 2 isoform X1

      Conserved Domains (1) summary
      pfam02301
      Location:31 → 228
      HORMA; HORMA domain

    5. XM_011529914.3 → XP_011528216.1  HORMA domain-containing protein 2 isoform X1

      See identical proteins and their annotated locations for XP_011528216.1

      Conserved Domains (1) summary
      pfam02301
      Location:31 → 228
      HORMA; HORMA domain

    6. XM_047441157.1 → XP_047297113.1  HORMA domain-containing protein 2 isoform X3

    7. XM_017028625.2 → XP_016884114.1  HORMA domain-containing protein 2 isoform X4

    8. XM_017028626.2 → XP_016884115.1  HORMA domain-containing protein 2 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      30541076..30670783
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054325133.1 → XP_054181108.1  HORMA domain-containing protein 2 isoform X1

    2. XM_054325135.1 → XP_054181110.1  HORMA domain-containing protein 2 isoform X2

      UniProtKB/Swiss-Prot
      B5MEB2, Q8N7B1, Q8NHR2

    3. XM_054325131.1 → XP_054181106.1  HORMA domain-containing protein 2 isoform X1

    4. XM_054325134.1 → XP_054181109.1  HORMA domain-containing protein 2 isoform X1

    5. XM_054325132.1 → XP_054181107.1  HORMA domain-containing protein 2 isoform X1

    6. XM_054325136.1 → XP_054181111.1  HORMA domain-containing protein 2 isoform X3

    7. XM_054325137.1 → XP_054181112.1  HORMA domain-containing protein 2 isoform X4

    8. XM_054325138.1 → XP_054181113.1  HORMA domain-containing protein 2 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N7B1.2 GenPept UniProtKB/Swiss-Prot:Q8N7B1

    Gene LinkOut

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

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