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

Gene ID: 285362, updated on 3-Apr-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
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Genomic context

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Location:
3p26.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (4034486..4467269, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (4027797..4461277, complement)
105.20220307 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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Related articles in PubMed

  1. Association between SUMF1 polymorphisms and COVID-19 severity. Liang S, et al. BMC Genom Data, 2023 Jun 21. PMID 37344788, Free PMC Article
  2. Natural history of multiple sulfatase deficiency: Retrospective phenotyping and functional variant analysis to characterize an ultra-rare disease. Adang LA, et al. J Inherit Metab Dis, 2020 Nov. PMID 32749716, Free PMC Article
  3. A systematic review and meta-analysis of published cases reveals the natural disease history in multiple sulfatase deficiency. Schlotawa L, et al. J Inherit Metab Dis, 2020 Nov. PMID 32621519
  4. Multiple Sulfatase Deficiency: A Disease Comprising Mucopolysaccharidosis, Sphingolipidosis, and More Caused by a Defect in Posttranslational Modification. Schlotawa L, et al. Int J Mol Sci, 2020 May 13. PMID 32414121, Free PMC Article
  5. A homozygous missense variant of SUMF1 in the Bedouin population extends the clinical spectrum in ultrarare neonatal multiple sulfatase deficiency. Staretz-Chacham O, et al. Mol Genet Genomic Med, 2020 Sep. PMID 32048457, Free PMC Article

See all (53) citations in PubMed

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
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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)

Genotypes

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 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
  

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_2023_10

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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