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    SLF2 SMC5-SMC6 complex localization factor 2 [ Homo sapiens (human) ]

    Gene ID: 55719, updated on 3-Apr-2024

    Summary

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    Official Symbol
    SLF2provided by HGNC
    Official Full Name
    SMC5-SMC6 complex localization factor 2provided by HGNC
    Primary source
    HGNC:HGNC:17814
    See related
    Ensembl:ENSG00000119906 MIM:610348; AllianceGenome:HGNC:17814
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ATELS1; C10orf6; FAM178A
    Summary
    Enables ubiquitin protein ligase binding activity. Involved in several processes, including positive regulation of cellular component organization; positive regulation of double-strand break repair; and protein localization to site of double-strand break. Located in chromatin; nucleoplasm; and site of double-strand break. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in testis (RPKM 12.5), ovary (RPKM 7.5) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    10q24.31
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (100912963..100965134)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (101792183..101848510)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (102672720..102724891)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:102321666-102322304 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:102322305-102322942 Neighboring gene hypoxia inducible factor 1 subunit alpha inhibitor Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:102401951-102402580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102421749-102422248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2708 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102440375-102440986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102443611-102444112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102447267-102447771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102473509-102474318 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:102496683-102497428 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:102497429-102498172 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3899 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102505530-102506071 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102509961-102510895 Neighboring gene paired box 2 Neighboring gene VISTA enhancer hs229 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102550131-102551044 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:102551431-102551607 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102562802-102563302 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102567263-102567763 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102576822-102577322 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:102606788-102607987 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2709 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:102633779-102634445 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr10:102649745-102650944 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2710 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3901 Neighboring gene Sharpr-MPRA regulatory region 3697 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2711 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3902 Neighboring gene semaphorin 4G Neighboring gene microRNA 608 Neighboring gene mitochondrial ribosomal protein L43

    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. cDNA cloning, expression profile and genomic structure of a novel human transcript on chromosome 10q24, and its analyses as a candidate gene for infantile onset spinocerebellar ataxia. Nikali K, et al. Gene, 2002 Oct 16. PMID 12459258
    2. Pathogenic variants in SLF2 and SMC5 cause segmented chromosomes and mosaic variegated hyperploidy. Grange LJ, et al. Nat Commun, 2022 Nov 4. PMID 36333305, Free PMC Article
    3. The Nse5/6-like SIMC1-SLF2 complex localizes SMC5/6 to viral replication centers. Oravcová M, et al. Elife, 2022 Nov 14. PMID 36373674, Free PMC Article
    4. Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components. Alabert C, et al. Nat Cell Biol, 2014 Mar. PMID 24561620, Free PMC Article
    5. Molecular Insights into the Architecture of the Human SMC5/6 Complex. Adamus M, et al. J Mol Biol, 2020 Jun 12. PMID 32389690

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Actionable loss of SLF2 drives B-cell lymphomagenesis and impairs the DNA damage response.
      Title: Actionable loss of SLF2 drives B-cell lymphomagenesis and impairs the DNA damage response.
    2. Pathogenic variants in SLF2 and SMC5 cause segmented chromosomes and mosaic variegated hyperploidy.
      Title: Pathogenic variants in SLF2 and SMC5 cause segmented chromosomes and mosaic variegated hyperploidy.
    3. ATRX proximal protein associations boast roles beyond histone deposition.
      Title: ATRX proximal protein associations boast roles beyond histone deposition.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
    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

    Associated conditions

    Description Tests
    Atelis syndrome 1
    MedGen: C5774281 OMIM: 620184 GeneReviews: Not available
    		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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC90157

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-containing complex binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin protein ligase binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in DNA damage response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in DNA damage response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in chromatin looping NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in double-strand break repair via homologous recombination NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of double-strand break repair IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of double-strand break repair IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of maintenance of mitotic sister chromatid cohesion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of protein-containing complex assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein localization to site of double-strand break IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein localization to site of double-strand break IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein sumoylation NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in regulation of telomere maintenance NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in PML body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of Smc5-Smc6 complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chromosome, telomeric region NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in intracellular membrane-bounded organelle 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 
    is_active_in site of double-strand break IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in site of double-strand break IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    SMC5-SMC6 complex localization factor protein 2
    Names
    family with sequence similarity 178, member A
    protein FAM178A
    smc5/6 localization factor 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.

    mRNA and Protein(s)

    1. NM_001136123.2 → NP_001129595.1  SMC5-SMC6 complex localization factor protein 2 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an exon and differs in the 3' UTR, compared to variant 1. The encoded isoform (2) is longer and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AF460992, BC030565
      Consensus CDS
      CCDS44470.1
      UniProtKB/Swiss-Prot
      Q8IX21
      Related
      ENSP00000359292.3, ENST00000370269.3
      Conserved Domains (1) summary
      pfam14816
      Location:661 → 1028
      FAM178; Family of unknown function, FAM178

    2. NM_001243770.2 → NP_001230699.1  SMC5-SMC6 complex localization factor protein 2 isoform 3

      See identical proteins and their annotated locations for NP_001230699.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) is unspliced, lacks a large portion of the coding region and differs in the 3' UTR, compared to variant 1. The encoded isoform (3) is significantly shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AA829402, AF460991, BC073832
      Consensus CDS
      CCDS65918.1
      UniProtKB/Swiss-Prot
      Q8IX21
      Related
      ENSP00000476379.1, ENST00000609386.1

    3. NM_018121.4 → NP_060591.3  SMC5-SMC6 complex localization factor protein 2 isoform 1

      See identical proteins and their annotated locations for NP_060591.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes isoform (1).
      Source sequence(s)
      AF460991, AI282394, BC030565
      Consensus CDS
      CCDS7500.1
      UniProtKB/Swiss-Prot
      A8K950, B1AL17, Q5W0L8, Q6GMU6, Q8IX21, Q9NPE8
      Related
      ENSP00000238961.3, ENST00000238961.9
      Conserved Domains (1) summary
      pfam14816
      Location:661 → 1028
      FAM178; Family of unknown function, FAM178

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      100912963..100965134
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047425461.1 → XP_047281417.1  SMC5-SMC6 complex localization factor protein 2 isoform X2

    2. XM_047425462.1 → XP_047281418.1  SMC5-SMC6 complex localization factor protein 2 isoform X3

    3. XM_011539944.4 → XP_011538246.1  SMC5-SMC6 complex localization factor protein 2 isoform X2

      Conserved Domains (1) summary
      pfam14816
      Location:597 → 964
      FAM178; Family of unknown function, FAM178

    4. XM_005269965.3 → XP_005270022.1  SMC5-SMC6 complex localization factor protein 2 isoform X1

      Conserved Domains (1) summary
      pfam14816
      Location:660 → 1027
      FAM178; Family of unknown function, FAM178

    5. XM_047425463.1 → XP_047281419.1  SMC5-SMC6 complex localization factor protein 2 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      101792183..101848510
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054366272.1 → XP_054222247.1  SMC5-SMC6 complex localization factor protein 2 isoform X2

    2. XM_054366274.1 → XP_054222249.1  SMC5-SMC6 complex localization factor protein 2 isoform X3

    3. XM_054366273.1 → XP_054222248.1  SMC5-SMC6 complex localization factor protein 2 isoform X2

    4. XM_054366271.1 → XP_054222246.1  SMC5-SMC6 complex localization factor protein 2 isoform X1

    5. XM_054366275.1 → XP_054222250.1  SMC5-SMC6 complex localization factor protein 2 isoform X4

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_144592.1: Suppressed sequence

      Description
      NM_144592.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript, and the CDS was partial.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IX21.2 GenPept UniProtKB/Swiss-Prot:Q8IX21

    Gene LinkOut

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

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