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    SUMF1 sulfatase modifying factor 1 [ Homo sapiens (human) ]

    Gene ID: 285362, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SUMF1provided by HGNC
    Official Full Name
    sulfatase modifying factor 1provided by HGNC
    Primary source
    HGNC:HGNC:20376
    See related
    Ensembl:ENSG00000144455 MIM:607939; AllianceGenome:HGNC:20376
    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
    FGE; UNQ3037; AAPA3037
    Summary
    This gene encodes an enzyme that catalyzes the hydrolysis of sulfate esters by oxidizing a cysteine residue in the substrate sulfatase to an active site 3-oxoalanine residue, which is also known as C-alpha-formylglycine. Mutations in this gene cause multiple sulfatase deficiency, a lysosomal storage disorder. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]
    Expression
    Ubiquitous expression in kidney (RPKM 5.9), thyroid (RPKM 5.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SUMF1 in Genome Data Viewer
    Location:
    3p26.1
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (4034486..4467269, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (4027797..4461277, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (4402830..4508953, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100130207 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14012 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14013 Neighboring gene Sharpr-MPRA regulatory region 107 Neighboring gene leucine rich repeat neuronal 1 Neighboring gene uncharacterized LOC102723512 Neighboring gene polyribonucleotide nucleotidyltransferase 1 pseudogene 1 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:4107004-4107504 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:4344650-4345392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19346 Neighboring gene Sharpr-MPRA regulatory region 4455 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:4417340-4417840 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:4417841-4418341 Neighboring gene Sharpr-MPRA regulatory region 6601 Neighboring gene SET domain and mariner transposase fusion gene Neighboring gene Sharpr-MPRA regulatory region 14120 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14015 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19347 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:4473683-4474469 Neighboring gene uncharacterized LOC124909340 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19348 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14017 Neighboring gene mitochondrial ribosomal protein S10 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14018 Neighboring gene Sharpr-MPRA regulatory region 12228 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19349 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19350 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19351 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19352 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:4555812-4556324 Neighboring gene Sharpr-MPRA regulatory region 14798 Neighboring gene ITPR1 divergent transcript Neighboring gene uncharacterized LOC124906344 Neighboring gene inositol 1,4,5-trisphosphate receptor type 1

    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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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SUMF1 overexpression promotes tumorous cell growth and migration and is correlated with the immune status of patients with glioma.
      Title: SUMF1 overexpression promotes tumorous cell growth and migration and is correlated with the immune status of patients with glioma.
    2. Association between SUMF1 polymorphisms and COVID-19 severity.
      Title: Association between SUMF1 polymorphisms and COVID-19 severity.
    3. Natural history of multiple sulfatase deficiency: Retrospective phenotyping and functional variant analysis to characterize an ultra-rare disease.
      Title: Natural history of multiple sulfatase deficiency: Retrospective phenotyping and functional variant analysis to characterize an ultra-rare disease.
    4. A systematic review and meta-analysis of published cases reveals the natural disease history in multiple sulfatase deficiency.
      Title: A systematic review and meta-analysis of published cases reveals the natural disease history in multiple sulfatase deficiency.
    5. A homozygous missense variant of SUMF1 in the Bedouin population extends the clinical spectrum in ultrarare neonatal multiple sulfatase deficiency.
      Title: A homozygous missense variant of SUMF1 in the Bedouin population extends the clinical spectrum in ultrarare neonatal multiple sulfatase deficiency.
    6. Multiple Sulfatase Deficiency: A Disease Comprising Mucopolysaccharidosis, Sphingolipidosis, and More Caused by a Defect in Posttranslational Modification.
      Title: Multiple Sulfatase Deficiency: A Disease Comprising Mucopolysaccharidosis, Sphingolipidosis, and More Caused by a Defect in Posttranslational Modification.
    7. protein disulfide isomerase (PDI) plays a pivotal role in the recognition and quality control of Multiple sulfatase deficiency-causing FGE variants.
      Title: Recognition and ER Quality Control of Misfolded Formylglycine-Generating Enzyme by Protein Disulfide Isomerase.
    8. Multiple sulfatase deficiency is an autosomal recessive lysosomal storage disorder due to a deficiency in formylglycine-generating enzyme, which is encoded by the Sulfatase Modifying Factor 1 ( SUMF1) gene.
      Title: Multiple Sulfatase Deficiency: A Case Series With a Novel Mutation.
    9. Herein, in this report, it was aimed to depict two rare cases from two different families with similar gene mutations and clinical presentation, neuro-imaging, and laboratory result of MSD in Iran.
      Title: The report of two cases with multiple sulfatase deficiency resulting from a rare similar gene mutation.
    10. We show that SUMF1 expression is affected in COPD patients compared to controls, and that SNPs in SUMF1 are associated with an increased risk of COPD. Certain COPD-associated SNPs have effects on either SUMF1 gene expression or on lung function. Collectively, this study shows that SUMF1 is associated with an increased risk of developing COPD.
      Title: Sulfatase modifying factor 1 (SUMF1) is associated with Chronic Obstructive Pulmonary Disease.
    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
    Multiple sulfatase deficiency
    MedGen: C0268263 OMIM: 272200 GeneReviews: Multiple Sulfatase Deficiency
    		Compare labs

    EBI GWAS Catalog

    Description
    Genetic variation influences glutamate concentrations in brains of patients with multiple sclerosis.
    EBI GWAS Catalog
    Genome-wide association study of chronic periodontitis in a general German population.
    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)

    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

    • MGC131853, MGC150436

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cupric ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables formylglycine-generating oxidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables formylglycine-generating oxidase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables oxidoreductase activity TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in glycosphingolipid catabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in post-translational protein modification IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in post-translational protein modification TAS
    Traceable Author Statement
    more info
    		  
    involved_in protein oxidation IDA
    Inferred from Direct Assay
    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
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    formylglycine-generating enzyme
    Names
    C-alpha-formylglycine-generating enzyme 1
    FGly-generating enzyme
    NP_001158146.1
    NP_001158147.1
    NP_877437.2
    XP_011531926.1
    XP_011531927.1
    XP_011531928.1
    XP_016861741.1
    XP_016861742.1
    XP_016861743.1
    XP_047303980.1
    XP_047303981.1
    XP_047303982.1
    XP_054202301.1
    XP_054202302.1
    XP_054202303.1
    XP_054202304.1
    XP_054202305.1
    XP_054202306.1
    XP_054202307.1
    XP_054202308.1
    XP_054202309.1

    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_016225.3 RefSeqGene

      Range
      5000..111123
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001164674.2 → NP_001158146.1  formylglycine-generating enzyme isoform 2 precursor

      See identical proteins and their annotated locations for NP_001158146.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
      Source sequence(s)
      AC034191, AK302018, CA413741, DA844846
      Consensus CDS
      CCDS54548.1
      UniProtKB/Swiss-Prot
      Q8NBK3
      Related
      ENSP00000373355.5, ENST00000383843.9
      Conserved Domains (2) summary
      TIGR03525
      Location:91 → 349
      GldK; gliding motility-associated lipoprotein GldK
      pfam03781
      Location:91 → 342
      FGE-sulfatase; Sulfatase-modifying factor enzyme 1

    2. NM_001164675.2 → NP_001158147.1  formylglycine-generating enzyme isoform 3 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
      Source sequence(s)
      AC034191, BC121123, CA413741, DA844846
      Consensus CDS
      CCDS54549.1
      UniProtKB/Swiss-Prot
      Q8NBK3
      Related
      ENSP00000384977.2, ENST00000405420.2
      Conserved Domains (2) summary
      TIGR03525
      Location:91 → 354
      GldK; gliding motility-associated lipoprotein GldK
      pfam03781
      Location:91 → 347
      FGE-sulfatase; Sulfatase-modifying factor enzyme 1

    3. NM_182760.4 → NP_877437.2  formylglycine-generating enzyme isoform 1 precursor

      See identical proteins and their annotated locations for NP_877437.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC034191, BC121122, CA413741
      Consensus CDS
      CCDS2564.1
      UniProtKB/Swiss-Prot
      B4DXK5, B7XD05, E9PGL0, G5E9B0, Q0VAC6, Q0VAC7, Q2NL78, Q53ZE4, Q6UY39, Q8NBK3, Q96AK5, Q96DK8
      UniProtKB/TrEMBL
      F5GXA0
      Related
      ENSP00000272902.5, ENST00000272902.10
      Conserved Domains (2) summary
      TIGR03525
      Location:91 → 374
      GldK; gliding motility-associated lipoprotein GldK
      pfam03781
      Location:91 → 367
      FGE-sulfatase; Sulfatase-modifying factor enzyme 1

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      4034486..4467269 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017006254.3 → XP_016861743.1  formylglycine-generating enzyme isoform X4

      UniProtKB/TrEMBL
      F5GXA0
      Related
      ENSP00000404384.1, ENST00000448413.5
      Conserved Domains (1) summary
      pfam03781
      Location:91 → 347
      FGE-sulfatase; Sulfatase-modifying factor enzyme 1

    2. XM_017006253.2 → XP_016861742.1  formylglycine-generating enzyme isoform X3

      UniProtKB/TrEMBL
      F5GXA0
      Conserved Domains (2) summary
      pfam03781
      Location:91 → 322
      FGE-sulfatase; Sulfatase-modifying factor enzyme 1
      cl17169
      Location:321 → 396
      RRM_SF; RNA recognition motif (RRM) superfamily

    3. XM_017006252.3 → XP_016861741.1  formylglycine-generating enzyme isoform X2

      UniProtKB/TrEMBL
      F5GXA0
      Conserved Domains (2) summary
      pfam03781
      Location:91 → 324
      FGE-sulfatase; Sulfatase-modifying factor enzyme 1
      cl17169
      Location:326 → 401
      RRM_SF; RNA recognition motif (RRM) superfamily

    4. XM_011533624.4 → XP_011531926.1  formylglycine-generating enzyme isoform X1

      UniProtKB/TrEMBL
      F5GXA0
      Conserved Domains (2) summary
      pfam03781
      Location:91 → 347
      FGE-sulfatase; Sulfatase-modifying factor enzyme 1
      cl17169
      Location:346 → 421
      RRM_SF; RNA recognition motif (RRM) superfamily

    5. XM_047448024.1 → XP_047303980.1  formylglycine-generating enzyme isoform X7

    6. XM_011533625.4 → XP_011531927.1  formylglycine-generating enzyme isoform X5

      Conserved Domains (1) summary
      pfam03781
      Location:91 → 339
      FGE-sulfatase; Sulfatase-modifying factor enzyme 1

    7. XM_011533626.4 → XP_011531928.1  formylglycine-generating enzyme isoform X6

      Conserved Domains (1) summary
      pfam03781
      Location:91 → 337
      FGE-sulfatase; Sulfatase-modifying factor enzyme 1

    8. XM_047448025.1 → XP_047303981.1  formylglycine-generating enzyme isoform X8

    9. XM_047448026.1 → XP_047303982.1  formylglycine-generating enzyme isoform X9

    RNA

    1. XR_007095664.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      4027797..4461277 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346329.1 → XP_054202304.1  formylglycine-generating enzyme isoform X4

    2. XM_054346328.1 → XP_054202303.1  formylglycine-generating enzyme isoform X3

    3. XM_054346327.1 → XP_054202302.1  formylglycine-generating enzyme isoform X2

    4. XM_054346326.1 → XP_054202301.1  formylglycine-generating enzyme isoform X1

    5. XM_054346332.1 → XP_054202307.1  formylglycine-generating enzyme isoform X7

    6. XM_054346330.1 → XP_054202305.1  formylglycine-generating enzyme isoform X5

    7. XM_054346331.1 → XP_054202306.1  formylglycine-generating enzyme isoform X6

    8. XM_054346333.1 → XP_054202308.1  formylglycine-generating enzyme isoform X8

    9. XM_054346334.1 → XP_054202309.1  formylglycine-generating enzyme isoform X9

    RNA

    1. XR_008486702.1 RNA Sequence

    2. XR_008486703.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NBK3.3 GenPept UniProtKB/Swiss-Prot:Q8NBK3

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