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

Gene ID: 3508, updated on 2-Nov-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
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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

Expression

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  • Project title: HPA RNA-seq normal tissues 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. Clinical variability in distal spinal muscular atrophy type 1 (DSMA1): determination of steady-state IGHMBP2 protein levels in five patients with infantile and juvenile disease. Guenther UP, et al. J Mol Med (Berl), 2009 Jan. PMID 18802676
  2. Recessive hereditary motor and sensory neuropathy caused by IGHMBP2 gene mutation. Shi CH, et al. Neurology, 2015 Jul 28. PMID 26136520, Free PMC Article
  3. [IGHMBP2 overexpression promotes cell migration and invasion in esophageal squamous carcinoma]. Wang CL, et al. Yi Chuan, 2015 Apr. PMID 25881701
  4. Recessive truncating IGHMBP2 mutations presenting as axonal sensorimotor neuropathy. Schottmann G, et al. Neurology, 2015 Feb 3. PMID 25568292
  5. Truncating and missense mutations in IGHMBP2 cause Charcot-Marie Tooth disease type 2. Cottenie E, et al. Am J Hum Genet, 2014 Nov 6. PMID 25439726, Free PMC Article

See all (73) citations in PubMed

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)

Genotypes

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 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 helicase activity TAS
Traceable Author Statement
more info
 PubMed 
enables RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables double-stranded DNA helicase activity IDA
Inferred from Direct Assay
more info
 PubMed 
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 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 
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

  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

  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

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