SKIC2 (SKI2 subunit of superkiller complex)

Gene

• Entrez ID: 6499
• Gene name: SKI2 subunit of superkiller complex
• Gene symbol: SKIC2
• Synonyms (NCBI Gene): 170A, DDX13, HLP, SKI2, SKI2W, SKIV2, SKIV2L, SKIV2L1, THES2
• Chromosome: 6
• Chromosome location: 6p21.33

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs200818962	C>T	Uncertain-significance, pathogenic	Coding sequence variant, stop gained, non coding transcript variant
rs750250320	C>T	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs751026211	G>A	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs766089213	G>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs768503878	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, stop gained, non coding transcript variant
rs781544014	C>T	Likely-pathogenic	Non coding transcript variant, 3 prime UTR variant, stop gained, coding sequence variant
rs781763471	A>G	Pathogenic	Splice acceptor variant
rs1562659544	->A	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1582171003	G>-	Not-provided, pathogenic	Stop gained, coding sequence variant, non coding transcript variant
rs1582187890	->A	Likely-pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT051423	hsa-let-7e-5p	CLASH	23622248
MIRT046701	hsa-miR-222-3p	CLASH	23622248
MIRT1351228	hsa-miR-3675-5p	CLIP-seq
MIRT1351229	hsa-miR-4307	CLIP-seq
MIRT1351230	hsa-miR-4666-5p	CLIP-seq
MIRT1351231	hsa-miR-4802-3p	CLIP-seq
MIRT1351232	hsa-miR-486-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003723	Function	RNA binding	IEA
GO:0003724	Function	RNA helicase activity	IBA
GO:0003724	Function	RNA helicase activity	IEA
GO:0003724	Function	RNA helicase activity	TAS	7610041
GO:0004386	Function	Helicase activity	IEA
GO:0005515	Function	Protein binding	IPI	32296183
GO:0005524	Function	ATP binding	IEA
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	TAS
GO:0006401	Process	RNA catabolic process	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0016887	Function	ATP hydrolysis activity	IEA
GO:0034458	Function	3'-5' RNA helicase activity	IDA	35120588
GO:0055087	Component	Ski complex	IBA
GO:0055087	Component	Ski complex	IDA	16024656, 32006463, 35120588
GO:0070478	Process	Nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay	IBA
GO:0070478	Process	Nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay	IDA	32006463, 35120588
GO:0072344	Process	Rescue of stalled ribosome	IDA	32006463

Other IDs

• MIM: 600478
• HGNC: 10898
• e!Ensembl: ENSG00000204351

Protein

• UniProt ID: Q15477
• Protein name: Superkiller complex protein 2 (Ski2) (EC 3.6.4.13) (Helicase-like protein) (HLP)
• Protein function: Helicase component of the SKI complex, a multiprotein complex that assists the RNA-degrading exosome during the mRNA decay and quality-control pathways (PubMed:16024656, PubMed:32006463, PubMed:35120588). The SKI complex catalyzes mRNA extractio
• PDB: 7QDR, 7QDS, 7QDY, 7QDZ, 7QE0, 9G8M, 9G8N, 9G8O, 9G8P, 9G8Q, 9G8R
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF17911	Ski2_N	74 → 203	Ski2 N-terminal region	Domain
  PF00270	DEAD	312 → 463	DEAD/DEAH box helicase	Domain
  PF00271	Helicase_C	563 → 708	Helicase conserved C-terminal domain	Family
  PF13234	rRNA_proc-arch	763 → 1046	rRNA-processing arch domain	Domain
  PF08148	DSHCT	1071 → 1240	DSHCT (NUC185) domain	Domain

• Sequence:

  MMETERLVLPPPDPLDLPLRAVELGCTGHWELLNLPGAPESSLPHGLPPCAPDLQQEAEQ
  LFLSSPAWLPLHGVEHSARKWQRKTDPWSLLAVLGAPVPSDLQAQRHPTTGQILGYKEVL
  LENTNLSATTSLSLRRPPGPASQSLWGNPTQYPFWPGGMDEPTITDLNTREEAEEEIDFE
  KDLLTIPPGFKKGMDFAPKDCPTPAPGLLSLSCMLEPLDLGGGDEDENEAVGQPGGPRGD
  TVSASPCSAPLARASSLEDLVLKEASTAVSTPEAPEPPSQEQWAIPVDATSPVGDFYRLI
  PQPAFQWAFEPDVFQKQAILHLERHDSVFVAAHTSAGKTVVAEYAIALAQKHMTRTIYTS
  PIKALSNQKFRDFRNTFGDVGLLTGDVQLHPEASCLIMTTEILRSMLYSGSDVIRDLEWV
  IFDEVHYINDVERGVVWEEVLIMLPDHVSIILLSATVPNALEFADWIGRLKRRQIYVIST
  VTRPVPLEHYLFTGNSSKTQGELFLLLDSRGAFHTKGYYAAVEAKKERMSKHAQTFGAKQ
  PTHQGGPAQDRGVYLSLLASLRTRAQLPVVVFTFSRGRCDEQASGLTSLDLTTSSEKSEI
  HLFLQRCLARLRGSDRQLPQVLHMSELLNRGLGVHHSGILPILKEIVEMLFSRGLVKVLF
  ATETFAMGVNMPARTVVFDSMRKHDGSTFRDLLPGEYVQMAGRAGRRGLDPTGTVILLCK
  GRVPEMADLHRMMMGKPSQLQSQFRLTYTMILNLLRVDALRVEDMMKRSFSEFPSRKDSK
  AHEQALAELTKRLGALEEPDMTGQLVDLPEYYSWGEELTETQHMIQRRIMESVNGLKSLS
  AGRVVVVKNQEHHNALGVILQVSSNSTSRVFTTLVLCDKPLSQDPQDRGPATAEVPYPDD
  LVGFKLFLPEGPCDHTVVKLQPGDMAAITTKVLRVNGEKILEDFSKRQQPKFKKDPPLAA
  VTTAVQELLRLAQAHPAGPPTLDPVNDLQLKDMSVVEGGLRARKLEELIQGAQCVHSPRF
  PAQYLKLRERMQIQKEMERLRFLLSDQSLLLLPEYHQRVEVLRTLGYVDEAGTVKLAGRV
  ACAMSSHELLLTELMFDNALSTLRPEEIAALLSGLVCQSPGDAGDQLPNTLKQGIERVRA
  VAKRIGEVQVACGLNQTVEEFVGELNFGLVEVVYEWARGMPFSELAGLSGTPEGLVVRCI
  QRLAEMCRSLRGAARLVGEPVLGAKMETAATLLRRDIVFAASLYTQ

• Sequence length: 1246

Pathways

KEGG:

RNA degradation

Reactome:

mRNA decay by 3' to 5' exoribonuclease

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Associated diseases

Causal
Disease merge term	Disease name	dbSNP ID	References
Trichohepatoenteric Syndrome	trichohepatoenteric syndrome 2	rs1582192007, rs751074844, rs770099418, rs751026211, rs1582171003, rs1562659544, rs200818962, rs781763471, rs768503878, rs1582187890	N/A

Unknown
Disease merge term	Disease name	Evidence	References	Source
Diabetes	Type 2 diabetes mellitus or coronary artery disease (pleiotropy)	N/A	N/A	GWAS
Macular Degeneration	Macular degeneration	N/A	N/A	GWAS