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    SUMF2 sulfatase modifying factor 2 [ Homo sapiens (human) ]

    Gene ID: 25870, updated on 3-Apr-2024

    Summary

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    Official Symbol
    SUMF2provided by HGNC
    Official Full Name
    sulfatase modifying factor 2provided by HGNC
    Primary source
    HGNC:HGNC:20415
    See related
    Ensembl:ENSG00000129103 MIM:607940; AllianceGenome:HGNC:20415
    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
    pFGE
    Summary
    The catalytic sites of sulfatases are only active if they contain a unique amino acid, C-alpha-formylglycine (FGly). The FGly residue is posttranslationally generated from a cysteine by enzymes with FGly-generating activity. The gene described in this record is a member of the sulfatase-modifying factor family and encodes a protein with a DUF323 domain that localizes to the lumen of the endoplasmic reticulum. This protein has low levels of FGly-generating activity but can heterodimerize with another family member - a protein with high levels of FGly-generating activity. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in thyroid (RPKM 45.6), kidney (RPKM 41.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SUMF2 in Genome Data Viewer
    Location:
    7p11.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (56064286..56087946)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (56224110..56247761)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (56131979..56148363)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene chaperonin containing TCP1 subunit 6A Neighboring gene small nucleolar RNA, H/ACA box 22B Neighboring gene Sharpr-MPRA regulatory region 2601 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18195 Neighboring gene small nucleolar RNA, H/ACA box 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26050 Neighboring gene Sharpr-MPRA regulatory region 7863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26051 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26052 Neighboring gene phosphorylase kinase catalytic subunit gamma 1 Neighboring gene uncharacterized LOC124901852 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:56171568-56172068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:56172069-56172569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26053 Neighboring gene coiled-coil-helix-coiled-coil-helix domain containing 2

    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. Expression, localization, structural, and functional characterization of pFGE, the paralog of the Calpha-formylglycine-generating enzyme. Mariappan M, et al. J Biol Chem, 2005 Apr 15. PMID 15708861
    2. Crystal structure of human pFGE, the paralog of the Calpha-formylglycine-generating enzyme. Dickmanns A, et al. J Biol Chem, 2005 Apr 15. PMID 15687489
    3. SUMF2 interacts with interleukin-13 and inhibits interleukin-13 secretion in bronchial smooth muscle cells. Liang H, et al. J Cell Biochem, 2009 Dec 1. PMID 19739097
    4. The multiple sulfatase deficiency gene encodes an essential and limiting factor for the activity of sulfatases. Cosma MP, et al. Cell, 2003 May 16. PMID 12757706
    5. Differential DNA methylation analysis of SUMF2, ADAMTS5, and PXDN provides novel insights into colorectal cancer prognosis prediction in Taiwan. Su JQ, et al. World J Gastroenterol, 2022 Feb 28. PMID 35317099, Free PMC Article

    See all (52) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Differential DNA methylation analysis of SUMF2, ADAMTS5, and PXDN provides novel insights into colorectal cancer prognosis prediction in Taiwan.
      Title: Differential DNA methylation analysis of SUMF2, ADAMTS5, and PXDN provides novel insights into colorectal cancer prognosis prediction in Taiwan.
    2. SUMF2 interacted with IL-13 and inhibited IL-13 secretion in bronchial smooth muscle cells and lymphocytes, which was independent of IL-13 glycosylation
      Title: SUMF2 interacts with interleukin-13 and inhibits interleukin-13 secretion in bronchial smooth muscle cells.
    3. pFGE is retained in the ER through its C-terminal tetrapeptide PGEL, a noncanonical variant of the classic KDEL ER-retention signal.
      Title: Paralog of the formylglycine-generating enzyme--retention in the endoplasmic reticulum by canonical and noncanonical signals.
    4. SUMF2 interacts with sulphatase-modifying factor 1 to regulate sulphatase activities.
      Title: Sulphatase activities are regulated by the interaction of sulphatase-modifying factor 1 with SUMF2.
    5. pFGE (SUMF2) is the paralog of the Calpha-formylglycine-generating enzyme
      Title: Expression, localization, structural, and functional characterization of pFGE, the paralog of the Calpha-formylglycine-generating enzyme.
    6. structural analysis of human pFGE by X-ray crystallography [pFGE]
      Title: Crystal structure of human pFGE, the paralog of the Calpha-formylglycine-generating enzyme.
    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
    Genome wide association study (GWAS) of Chagas cardiomyopathy in Trypanosoma cruzi seropositive subjects.
    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
    Envelope surface glycoprotein gp120 env HIV-1 gp120 is identified to have a physical interaction with sulfatase modifying factor 2 (SUMF2) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
    Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with SUMF2; predicted interaction to be within the endoplasmic reticulum 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

    • MGC99485, DKFZp566I1024, DKFZp686I1024, DKFZp781L1035, DKFZp686L17160

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    inactive C-alpha-formylglycine-generating enzyme 2
    Names
    C-alpha-formyglycine-generating enzyme 2
    C-alpha-formylglycine-generating enzyme 2
    epididymis secretory sperm binding protein
    paralog of formylglycine-generating enzyme
    paralog of the formylglycine-generating enzyme

    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_001042468.3 → NP_001035933.3  inactive C-alpha-formylglycine-generating enzyme 2 isoform a precursor

      Status: REVIEWED

      Source sequence(s)
      BC084539, BP256067, BP296294, CR936757, DA130450, KU178583
      UniProtKB/TrEMBL
      B4DLK7
      Conserved Domains (1) summary
      pfam03781
      Location:26 → 295
      FGE-sulfatase; Sulfatase-modifying factor enzyme 1

    2. NM_001042469.3 → NP_001035934.3  inactive C-alpha-formylglycine-generating enzyme 2 isoform c precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the mid coding region, compared to variant 2, resulting in a shorter protein (isoform c), compared to isoform b.
      Source sequence(s)
      BC084539, BP296294, CR936749, CR936757, KU178583
      Consensus CDS
      CCDS43588.3
      UniProtKB/TrEMBL
      A8MXB9, B4DLK7
      Related
      ENSP00000498981.1, ENST00000651586.1
      Conserved Domains (1) summary
      pfam03781
      Location:26 → 277
      FGE-sulfatase; Sulfatase-modifying factor enzyme 1

    3. NM_001042470.3 → NP_001035935.3  inactive C-alpha-formylglycine-generating enzyme 2 isoform d precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks three alternate exons that causes the absence of an in-frame segment in the mid coding region, compared to variant 2. The resulting isoform (d) is shorter than isoform b.
      Source sequence(s)
      BC084539, BP296294, CR936757, DA917807, KU178583
      Consensus CDS
      CCDS43589.3
      UniProtKB/TrEMBL
      E9PBT8
      Related
      ENSP00000498997.1, ENST00000650735.1
      Conserved Domains (1) summary
      cl23855
      Location:26 → 208
      FGE-sulfatase; Sulfatase-modifying factor enzyme 1

    4. NM_001130069.4 → NP_001123541.2  inactive C-alpha-formylglycine-generating enzyme 2 isoform e precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks the penultimate coding exon, compared to variant 2, resulting in a frameshift and a protein (isoform e) with a longer and distinct C-terminus when compared to isoform b.
      Source sequence(s)
      BC000224, BC015600, DA924174, KU178583
      Consensus CDS
      CCDS47589.2
      UniProtKB/TrEMBL
      F8WA42
      Related
      ENSP00000341938.7, ENST00000342190.11
      Conserved Domains (1) summary
      pfam03781
      Location:26 → 226
      FGE-sulfatase; Sulfatase-modifying factor enzyme 1

    5. NM_001146333.3 → NP_001139805.1  inactive C-alpha-formylglycine-generating enzyme 2 isoform g

      See identical proteins and their annotated locations for NP_001139805.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon, compared to variant 2. The encoded isoform (g) is shorter than isoform b.
      Source sequence(s)
      BC000224, BC065222, DA924174
      Consensus CDS
      CCDS55111.1
      Related
      ENSP00000275607.9, ENST00000275607.13
      Conserved Domains (2) summary
      COG1262
      Location:8 → 207
      YfmG; Formylglycine-generating enzyme, required for sulfatase activity, contains SUMF1/FGE domain [Posttranslational modification, protein turnover, chaperones]
      pfam03781
      Location:8 → 204
      FGE-sulfatase; Sulfatase-modifying factor enzyme 1

    6. NM_001366647.2 → NP_001353576.1  inactive C-alpha-formylglycine-generating enzyme 2 isoform h precursor

      Status: REVIEWED

      Source sequence(s)
      AC092101, BP357420, CV379204, DA581576
      Conserved Domains (1) summary
      pfam03781
      Location:26 → 259
      FGE-sulfatase; Sulfatase-modifying factor enzyme 1

    7. NM_001366648.2 → NP_001353577.1  inactive C-alpha-formylglycine-generating enzyme 2 isoform i precursor

      Status: REVIEWED

      Source sequence(s)
      AC092101, BQ431971, DB260494, DB294596
      Consensus CDS
      CCDS94107.1
      UniProtKB/TrEMBL
      C9J660
      Related
      ENSP00000406445.1, ENST00000413756.5
      Conserved Domains (1) summary
      pfam03781
      Location:26 → 274
      FGE-sulfatase; Sulfatase-modifying factor enzyme 1

    8. NM_001366649.2 → NP_001353578.1  inactive C-alpha-formylglycine-generating enzyme 2 isoform j

      Status: REVIEWED

      Source sequence(s)
      AC092101, AL528271, DA908093

    9. NM_015411.4 → NP_056226.3  inactive C-alpha-formylglycine-generating enzyme 2 isoform b precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents the longest transcript and encodes isoform b.
      Source sequence(s)
      AK075477, BC084539, BP296294, CR936757, KU178583
      Consensus CDS
      CCDS5524.3
      UniProtKB/Swiss-Prot
      B4DU41, B4DWQ0, Q14DW5, Q53ZE3, Q8NBJ7, Q96BH2, Q9BRN3, Q9BWI1, Q9Y405
      UniProtKB/TrEMBL
      B4DLK7
      Related
      ENSP00000400922.3, ENST00000434526.8
      Conserved Domains (1) summary
      pfam03781
      Location:26 → 292
      FGE-sulfatase; Sulfatase-modifying factor enzyme 1

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      56064286..56087946
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047420120.1 → XP_047276076.1  inactive C-alpha-formylglycine-generating enzyme 2 isoform X1

      Related
      ENSP00000414434.3, ENST00000413952.7

    2. XM_047420122.1 → XP_047276078.1  inactive C-alpha-formylglycine-generating enzyme 2 isoform X2

    3. XM_011515254.4 → XP_011513556.2  inactive C-alpha-formylglycine-generating enzyme 2 isoform X1

    4. XM_047420121.1 → XP_047276077.1  inactive C-alpha-formylglycine-generating enzyme 2 isoform X2

    5. XM_047420123.1 → XP_047276079.1  inactive C-alpha-formylglycine-generating enzyme 2 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      56224110..56247761
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054357769.1 → XP_054213744.1  inactive C-alpha-formylglycine-generating enzyme 2 isoform X1

    2. XM_054357771.1 → XP_054213746.1  inactive C-alpha-formylglycine-generating enzyme 2 isoform X2

    3. XM_054357768.1 → XP_054213743.1  inactive C-alpha-formylglycine-generating enzyme 2 isoform X1

    4. XM_054357770.1 → XP_054213745.1  inactive C-alpha-formylglycine-generating enzyme 2 isoform X2

    5. XM_054357772.1 → XP_054213747.1  inactive C-alpha-formylglycine-generating enzyme 2 isoform X3

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001130070.1: Suppressed sequence

      Description
      NM_001130070.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NBJ7.2 GenPept UniProtKB/Swiss-Prot:Q8NBJ7

    Gene LinkOut

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

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