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SKIC2 SKI2 subunit of superkiller complex [ Homo sapiens (human) ]

Gene ID: 6499, updated on 7-Apr-2024

Summary

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Official Symbol
SKIC2provided by HGNC
Official Full Name
SKI2 subunit of superkiller complexprovided by HGNC
Primary source
HGNC:HGNC:10898
See related
Ensembl:ENSG00000204351 MIM:600478; AllianceGenome:HGNC:10898
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
HLP; 170A; SKI2; DDX13; SKI2W; SKIV2; THES2; SKIV2L; SKIV2L1
Summary
DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene encodes a DEAD box protein, which is a human homologue of yeast SKI2 and may be involved in antiviral activity by blocking translation of poly(A) deficient mRNAs. This gene is located in the class III region of the major histocompatibility complex. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in spleen (RPKM 10.8), lymph node (RPKM 9.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
6p21.33
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (31959175..31969751)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (31812380..31822956)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31926952..31937528)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:31915103-31915602 Neighboring gene complement factor B Neighboring gene negative elongation factor complex member E Neighboring gene microRNA 1236 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:31929542-31930741 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31939702-31940412 Neighboring gene serine/threonine kinase 19 Neighboring gene decapping exoribonuclease Neighboring gene complement C4A (Chido/Rodgers blood group)

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 SKIV2L polymorphism rs429608 and age-related macular degeneration: A meta-analysis. Shuai P, et al. Ophthalmic Genet, 2017 May-Jun. PMID 27484132
  2. Targeted next-generation sequencing identification of a novel missense mutation of the SKIV2L gene in a patient with trichohepatoenteric syndrome. Zheng B, et al. Mol Med Rep, 2016 Sep. PMID 27431780
  3. Expanding phenotypic and allelic heterogeneity of tricho-hepato-enteric syndrome. Monies DM, et al. J Pediatr Gastroenterol Nutr, 2015 Mar. PMID 25714577
  4. Genetic variants in the SKIV2L gene in exudative age-related macular degeneration in the Japanese population. Yoneyama S, et al. Ophthalmic Genet, 2014 Sep. PMID 24865191
  5. Associations of the C2-CFB-RDBP-SKIV2L locus with age-related macular degeneration and polypoidal choroidal vasculopathy. Liu K, et al. Ophthalmology, 2013 Apr. PMID 23260260

See all (89) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. We then examined the lab diagnostic cohort in detail for clinical manifestations. For the first time, we are able to suggest that patients lacking SKIV2L seem more severely affected than those lacking TTC37, in terms of liver damage and prenatal growth impairment.
    Title: Tricho-Hepato-Enteric Syndrome mutation update: Mutations spectrum of TTC37 and SKIV2L, clinical analysis and future prospects.
  2. This meta-analysis showed that SKIV2L rs429608 was statistically associated with age-related macular degeneration(AMD) and it might exert a protective effect on AMD. Further investigations are needed to validate the association and confirm the role of SKIV2L in AMD.
    Title: Association between SKIV2L polymorphism rs429608 and age-related macular degeneration: A meta-analysis.
  3. The present study was the first, to the best of our knowledge, to report a case of a boy with THES resulting from compound heterozygous mutations of the SKIV2L gene in China.
    Title: Targeted next-generation sequencing identification of a novel missense mutation of the SKIV2L gene in a patient with trichohepatoenteric syndrome.
  4. Study reported three point mutations, which have not been previously described in other patients with THES in SKIV2L and TTC37 genes, including one nonsense, one frameshift, and one missense mutations.
    Title: Novel mutations in SKIV2L and TTC37 genes in Malaysian children with trichohepatoenteric syndrome.
  5. Data from 4 consanguineous families in Saudi Arabia suggest SKIV2L mutations in tricho-hepato-enteric syndrome can include deletions (c.3559_3579del, p.1187_1193del; 4 subjects) and nonsense mutation (c.C4102T, p.Q1368X; 1 subject). [CASE REPORT]
    Title: Expanding phenotypic and allelic heterogeneity of tricho-hepato-enteric syndrome.
  6. A SKIV2L variant was associated with protection against exudative age-related macular degeneration regardless of subtypes in the Japanese population.
    Title: Genetic variants in the SKIV2L gene in exudative age-related macular degeneration in the Japanese population.
  7. Novel homozygous frameshift mutations in the AKR1D1 gene and in the SKIV2L gene were found in a family with severe infantile liver disease.
    Title: A combination of mutations in AKR1D1 and SKIV2L in a family with severe infantile liver disease.
  8. SKIV2L is a likely causal gene for neovascular AMD, conferring a significant protective effect independent of CFH and HTRA1.
    Title: Associations of the C2-CFB-RDBP-SKIV2L locus with age-related macular degeneration and polypoidal choroidal vasculopathy.
  9. The results showed that mutations in genes encoding SKIV2L cause trichohepatoenteric syndrome, establishing a link between defects of the human exosome complex and a Mendelian disease.
    Title: SKIV2L mutations cause syndromic diarrhea, or trichohepatoenteric syndrome.
  10. A protective effect was observed at rs429608, an intronic SNP in SKIV2L.
    Title: Genome-wide association identifies SKIV2L and MYRIP as protective factors for age-related macular degeneration.
Submit: New GeneRIF Correction See all GeneRIFs (15)

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
Trichohepatoenteric syndrome 2
MedGen: C3281289 OMIM: 614602 GeneReviews: Trichohepatoenteric Syndrome
Compare labs

EBI GWAS Catalog

Description
A novel common variant in DCST2 is associated with length in early life and height in adulthood.
EBI GWAS Catalog
An atlas of genetic influences on human blood metabolites.
EBI GWAS Catalog
Genetic factors in nonsmokers with age-related macular degeneration revealed through genome-wide gene-environment interaction analysis.
EBI GWAS Catalog
Genetic variants near TIMP3 and high-density lipoprotein-associated loci influence susceptibility to age-related macular degeneration.
EBI GWAS Catalog
Genome-wide association identifies SKIV2L and MYRIP as protective factors for age-related macular degeneration.
EBI GWAS Catalog
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
EBI GWAS Catalog
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
EBI GWAS Catalog
Seven new loci associated with age-related macular degeneration.
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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 3'-5' RNA helicase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
  
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in rescue of stalled ribosome IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of Ski complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of Ski complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
superkiller complex protein 2
Names
SKI2 homolog, superkiller viralicidic activity 2-like
SKI2 subunit of superkiller complex protein
Ski2 like RNA helicase
helicase SKI2W
helicase-like protein
superkiller viralicidic activity 2-like
NP_008860.4
XP_011513117.1
XP_047275215.1
XP_047275216.1
XP_054185828.1
XP_054185829.1
XP_054185830.1
XP_054186311.1
XP_054186312.1
XP_054186313.1
XP_054186827.1
XP_054186828.1
XP_054186829.1
XP_054187089.1
XP_054187090.1
XP_054187091.1
XP_054187350.1
XP_054187351.1
XP_054187352.1
XP_054212214.1
XP_054212215.1
XP_054212216.1

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_032652.1 RefSeqGene

    Range
    5372..15948
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_006929.5 → NP_008860.4  superkiller complex protein 2

    See identical proteins and their annotated locations for NP_008860.4

    Status: REVIEWED

    Source sequence(s)
    AL529319, BE395851, BG396326, U09877, Z48796
    Consensus CDS
    CCDS4731.1
    UniProtKB/Swiss-Prot
    O15005, Q12902, Q15476, Q15477, Q5ST66
    UniProtKB/TrEMBL
    A0A1U9X8J0, A0A1U9X8J1, Q9NPK3
    Related
    ENSP00000364543.2, ENST00000375394.7
    Conserved Domains (1) summary
    cl28230
    Location:280 → 1244
    Dob10; Superfamily II RNA helicase [Replication, recombination and repair]

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    31959175..31969751
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011514815.4 → XP_011513117.1  superkiller complex protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011513117.1

    UniProtKB/TrEMBL
    A0A8V8TLC0, A0A8V8TLR3
    Related
    ENSP00000513454.1, ENST00000697833.1
    Conserved Domains (4) summary
    smart00490
    Location:626 → 708
    HELICc; helicase superfamily c-terminal domain
    smart00487
    Location:309 → 486
    DEXDc; DEAD-like helicases superfamily
    pfam00270
    Location:315 → 462
    DEAD; DEAD/DEAH box helicase
    pfam13234
    Location:765 → 1023
    rRNA_proc-arch; rRNA-processing arch domain

  2. XM_047419259.1 → XP_047275215.1  superkiller complex protein 2 isoform X2

    UniProtKB/TrEMBL
    H7C5N0
    Related
    ENSP00000420332.2, ENST00000483553.6

  3. XM_047419260.1 → XP_047275216.1  superkiller complex protein 2 isoform X3

    Related
    ENSP00000513456.1, ENST00000697837.1

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    3436602..3447178
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054329853.1 → XP_054185828.1  superkiller complex protein 2 isoform X1

    UniProtKB/TrEMBL
    A0A8V8TLC0

  2. XM_054329854.1 → XP_054185829.1  superkiller complex protein 2 isoform X2

    UniProtKB/TrEMBL
    H7C5N0

  3. XM_054329855.1 → XP_054185830.1  superkiller complex protein 2 isoform X3

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    3206950..3217526
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330336.1 → XP_054186311.1  superkiller complex protein 2 isoform X1

  2. XM_054330337.1 → XP_054186312.1  superkiller complex protein 2 isoform X2

  3. XM_054330338.1 → XP_054186313.1  superkiller complex protein 2 isoform X3

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    3301211..3311787
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330853.1 → XP_054186828.1  superkiller complex protein 2 isoform X2

  2. XM_054330852.1 → XP_054186827.1  superkiller complex protein 2 isoform X1

  3. XM_054330854.1 → XP_054186829.1  superkiller complex protein 2 isoform X3

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    3215145..3225721
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331115.1 → XP_054187090.1  superkiller complex protein 2 isoform X2

  2. XM_054331114.1 → XP_054187089.1  superkiller complex protein 2 isoform X1

  3. XM_054331116.1 → XP_054187091.1  superkiller complex protein 2 isoform X3

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    3260364..3270940
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331376.1 → XP_054187351.1  superkiller complex protein 2 isoform X2

  2. XM_054331375.1 → XP_054187350.1  superkiller complex protein 2 isoform X1

  3. XM_054331377.1 → XP_054187352.1  superkiller complex protein 2 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    31812380..31822956
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054356240.1 → XP_054212215.1  superkiller complex protein 2 isoform X2

  2. XM_054356239.1 → XP_054212214.1  superkiller complex protein 2 isoform X1

  3. XM_054356241.1 → XP_054212216.1  superkiller complex protein 2 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q15477.3 GenPept UniProtKB/Swiss-Prot:Q15477

Gene LinkOut

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