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

Gene ID: 150280, updated on 5-Mar-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 sister chromatid cohesion. Located in centrosome; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Restricted expression toward testis (RPKM 6.8) See more
Orthologs
mouse all
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Genomic context

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Location:
22q12.2
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (30077732..30207456)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (30541076..30670783)
105.20220307 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. 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
  2. Genome-wide association study identifies variants in HORMAD2 associated with tonsillectomy. Feenstra B, et al. J Med Genet, 2017 May. PMID 27941131
  3. 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
  4. 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
  5. Identification of susceptibility locus shared by IgA nephropathy and inflammatory bowel disease in a Chinese Han population. Shi D, et al. J Hum Genet, 2020 Mar. PMID 31857673

See all (19) 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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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 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)

Genotypes

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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NEW Try the new Transcript table

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_2023_10

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

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