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

Gene ID: 55719, updated on 2-Nov-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 PML body; chromatin; and site of double-strand break. Implicated in mosaic variegated aneuploidy syndrome. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in testis (RPKM 12.5), ovary (RPKM 7.5) and 24 other tissues See more
Orthologs
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Genomic context

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See SLF2 in Genome Data Viewer
Location:
10q24.31
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (100912963..100965134)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (101792183..101848510)
RS_2024_09 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 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. Actionable loss of SLF2 drives B-cell lymphomagenesis and impairs the DNA damage response. Zhang L, et al. EMBO Mol Med, 2023 Sep 11. PMID 37485814, Free PMC Article
  3. 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
  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 (39) 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 
located_in 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_2024_08

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

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