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    IGHMBP2 immunoglobulin mu DNA binding protein 2 [ Homo sapiens (human) ]

    Gene ID: 3508, updated on 10-Dec-2024

    Summary

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    Official Symbol
    IGHMBP2provided by HGNC
    Official Full Name
    immunoglobulin mu DNA binding protein 2provided by HGNC
    Primary source
    HGNC:HGNC:5542
    See related
    Ensembl:ENSG00000132740 MIM:600502; AllianceGenome:HGNC:5542
    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
    HCSA; HMN6; CATF1; CMT2S; HMNR1; SMARD1; SMUBP2; ZFAND7
    Summary
    This gene encodes a helicase superfamily member that binds a specific DNA sequence from the immunoglobulin mu chain switch region. Mutations in this gene lead to spinal muscle atrophy with respiratory distress type 1. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in testis (RPKM 9.6), endometrium (RPKM 3.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See IGHMBP2 in Genome Data Viewer
    Location:
    11q13.3
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (68903891..68940601)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (68913020..68949716)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (68671359..68708069)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 2701 Neighboring gene mitochondrial ribosomal protein L21 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:68671173-68671900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5147 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5148 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:68701479-68702678 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:68714105-68714968 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5149 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68747435-68747944 Neighboring gene MAS related GPR family member D Neighboring gene ReSE screen-validated silencer GRCh37_chr11:68762134-68762300 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68769878-68770378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68771339-68771840 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:68775087-68775794 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:68775901-68777100 Neighboring gene MRGPRF antisense RNA 1 Neighboring gene MAS related GPR family member F

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. IGHMBP2 deletion suppresses translation and activates the integrated stress response.
      Title: IGHMBP2 deletion suppresses translation and activates the integrated stress response.
    2. RNA helicase IGHMBP2 regulates THO complex to ensure cellular mRNA homeostasis.
      Title: RNA helicase IGHMBP2 regulates THO complex to ensure cellular mRNA homeostasis.
    3. Validation of the Pathogenic Effect of IGHMBP2 Gene Mutations Based on Yeast S. cerevisiae Model.
      Title: Validation of the Pathogenic Effect of IGHMBP2 Gene Mutations Based on Yeast S. cerevisiae Model.
    4. Clinical and genetic features of Charcot-Marie-Tooth disease patients with IGHMBP2 mutations.
      Title: Clinical and genetic features of Charcot-Marie-Tooth disease patients with IGHMBP2 mutations.
    5. Charcot-Marie-Tooth disease type 2S: identical novel missense mutation of IGHMBP2 gene in two unrelated families.
      Title: Charcot-Marie-Tooth disease type 2S: identical novel missense mutation of IGHMBP2 gene in two unrelated families.
    6. We identified a paternally derived splice donor site mutation and a maternally derived missense mutation of IGHMBP2
      Title: Spinal muscular atrophy with respiratory distress type 1 associated with novel compound heterozygous mutations in IGHMBP2: Differential diagnosis in a case with congenital diaphragm eventration.
    7. UPF1, a highly processive helicase central to nonsense-mediated mRNA decay (NMD), tightly holds onto NA, allowing long lasting action. Conversely, the structurally similar IGHMBP2 helicase has a short residence time.
      Title: UPF1-like helicase grip on nucleic acids dictates processivity.
    8. detected IGHMBP2 mutations in a cohort of Chinese Charcot-Marie-Tooth disease type 2 patients; four mutations, c.1489G > A, c.2356delG, c.2597_2598delAG and c.1061-2A > G, are reported for the first time
      Title: IGHMBP2-related clinical and genetic features in a cohort of Chinese Charcot-Marie-Tooth disease type 2 patients.
    9. We present the original report of Charcot-Marie-Tooth disease (CMT) type 2S in Japan, and illustrate that recessive IGHMBP2 variants account for ~1.6% of axonal CMT in our cohort.
      Title: Clinical diversity caused by novel IGHMBP2 variants.
    10. Case report and review of 20 reported spinal muscular atrophy with respiratory distress type I cases that have no respiratory involvement or have late onsets, propose that IGHMBP2 gene mutations are characterized by significant phenotypic heterogeneity
      Title: Infantile spinal muscular atrophy with respiratory distress type I presenting without respiratory involvement: Novel mutations and review of the literature.
    Submit: New GeneRIF Correction See all GeneRIFs (33)

    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
    Autosomal recessive distal spinal muscular atrophy 1
    MedGen: C1858517 OMIM: 604320 GeneReviews: Not available
    		not available
    Charcot-Marie-Tooth disease axonal type 2S
    MedGen: C4015349 OMIM: 616155 GeneReviews: Not available
    		not available
    Charcot-Marie-Tooth disease type 2
    MedGen: C0270914 GeneReviews: Charcot-Marie-Tooth Hereditary Neuropathy Overview
    		not available

    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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    Replication interactions

    Interaction Pubs
    Knockdown of immunoglobulin mu binding protein 2 (IGHMBP2) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ34220, FLJ41171

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 5'-3' DNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 5'-3' DNA helicase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables 5'-3' RNA helicase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ATP binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ATP hydrolysis activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ATP-dependent H2AZ histone chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H3-H4 histone complex chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent activity, acting on DNA IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ATP-dependent activity, acting on RNA IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA clamp loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA helicase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cohesin loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables double-stranded DNA helicase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables forked DNA-dependent helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables four-way junction helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ribosome binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables single-stranded 3'-5' DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables single-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables single-stranded RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables tRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA duplex unwinding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in RNA secondary structure unwinding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in chromatin looping IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in axon ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in growth cone ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in membrane HDA PubMed 
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of ribonucleoprotein complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    DNA-binding protein SMUBP-2
    Names
    ATP-dependent helicase IGHMBP2
    GF-1
    cardiac transcription factor 1
    glial factor 1
    immunoglobulin mu binding protein 2
    zinc finger, AN1-type domain 7
    NP_002171.2
    XP_005274032.1
    XP_005274033.1
    XP_011543296.1
    XP_016873159.1
    XP_016873160.1
    XP_047282837.1
    XP_054224636.1
    XP_054224637.1
    XP_054224638.1
    XP_054224639.1
    XP_054224640.1
    XP_054224641.1

    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_007976.1 RefSeqGene

      Range
      5001..41751
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_250

    mRNA and Protein(s)

    1. NM_002180.3 → NP_002171.2  DNA-binding protein SMUBP-2

      See identical proteins and their annotated locations for NP_002171.2

      Status: REVIEWED

      Source sequence(s)
      BC025299, BE302389, DB448398, L14754
      Consensus CDS
      CCDS8187.1
      UniProtKB/Swiss-Prot
      A0PJD2, P38935, Q00443, Q14177
      UniProtKB/TrEMBL
      A0A6Q8PGT6
      Related
      ENSP00000255078.4, ENST00000255078.8
      Conserved Domains (6) summary
      cd02641
      Location:726 → 784
      R3H_Smubp-2_like; R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most ...
      TIGR00376
      Location:19 → 641
      TIGR00376; DNA helicase, putative
      pfam01428
      Location:897 → 934
      zf-AN1; AN1-like Zinc finger
      pfam12300
      Location:766 → 850
      DUF3628; Protein of unknown function (DUF3628)
      pfam13087
      Location:418 → 615
      AAA_12; AAA domain
      pfam13245
      Location:198 → 256
      AAA_19; Part of AAA 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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      68903891..68940601
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047426881.1 → XP_047282837.1  DNA-binding protein SMUBP-2 isoform X1

      UniProtKB/TrEMBL
      A0A6Q8PGT6

    2. XM_017017671.3 → XP_016873160.1  DNA-binding protein SMUBP-2 isoform X5

    3. XM_005273976.3 → XP_005274033.1  DNA-binding protein SMUBP-2 isoform X6

      Conserved Domains (2) summary
      pfam13086
      Location:192 → 410
      AAA_11; AAA domain
      pfam13245
      Location:198 → 256
      AAA_19; Part of AAA domain

    4. XM_017017670.3 → XP_016873159.1  DNA-binding protein SMUBP-2 isoform X2

      Conserved Domains (4) summary
      cd02641
      Location:389 → 447
      R3H_Smubp-2_like; R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most ...
      pfam01428
      Location:560 → 597
      zf-AN1; AN1-like Zinc finger
      pfam07793
      Location:448 → 522
      DUF1631; Protein of unknown function (DUF1631)
      pfam13087
      Location:81 → 278
      AAA_12; AAA domain

    5. XM_005273975.4 → XP_005274032.1  DNA-binding protein SMUBP-2 isoform X3

      Conserved Domains (4) summary
      cd02641
      Location:350 → 408
      R3H_Smubp-2_like; R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most ...
      pfam01428
      Location:521 → 558
      zf-AN1; AN1-like Zinc finger
      pfam07793
      Location:409 → 483
      DUF1631; Protein of unknown function (DUF1631)
      pfam13087
      Location:42 → 239
      AAA_12; AAA domain

    6. XM_011544994.2 → XP_011543296.1  DNA-binding protein SMUBP-2 isoform X4

      Conserved Domains (4) summary
      cd02641
      Location:315 → 373
      R3H_Smubp-2_like; R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most ...
      pfam01428
      Location:486 → 523
      zf-AN1; AN1-like Zinc finger
      pfam07793
      Location:374 → 448
      DUF1631; Protein of unknown function (DUF1631)
      pfam13087
      Location:7 → 204
      AAA_12; AAA domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      68913020..68949716
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054368661.1 → XP_054224636.1  DNA-binding protein SMUBP-2 isoform X1

      UniProtKB/TrEMBL
      A0A6Q8PGT6

    2. XM_054368665.1 → XP_054224640.1  DNA-binding protein SMUBP-2 isoform X5

    3. XM_054368666.1 → XP_054224641.1  DNA-binding protein SMUBP-2 isoform X6

    4. XM_054368662.1 → XP_054224637.1  DNA-binding protein SMUBP-2 isoform X2

    5. XM_054368663.1 → XP_054224638.1  DNA-binding protein SMUBP-2 isoform X3

    6. XM_054368664.1 → XP_054224639.1  DNA-binding protein SMUBP-2 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P38935.3 GenPept UniProtKB/Swiss-Prot:P38935

    Gene LinkOut

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

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