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

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Gastric cancer	Likely pathogenic	rs762751779	RCV005912589
Immunodeficiency 57	Pathogenic	rs767084483	RCV004999788
Ovarian serous cystadenocarcinoma	Likely pathogenic	rs1419680561, rs1375849231	RCV005934624 RCV005936616
SKIC2-related disorder	Pathogenic; Likely pathogenic	rs138923214, rs1353707093, rs200818962, rs2482913862, rs2482998760, rs751026211	RCV003956370 RCV003407950 RCV004752805 RCV003429065 RCV003911543 RCV003390696
Trichohepatoenteric syndrome	Pathogenic; Likely pathogenic	rs138923214, rs759511516, rs200271795, rs1772636752, rs2483002672, rs1244156082, rs899709021, rs377014444, rs2482913862	RCV003155429 RCV003155397 RCV001844644 RCV002240109 RCV002470082 RCV003123466 RCV003155841 RCV003226784 RCV006269838
Trichohepatoenteric syndrome 2	Pathogenic; Likely pathogenic	rs138923214, rs759511516, rs1772848223, rs750724648, rs1772679892, rs2482893792, rs1475859257, rs200818962, rs144714933, rs969421193, rs751026211, rs281875237, rs1562659544, rs781763471, rs768503878, rs1582187890, rs1582192007, rs751074844, rs770099418, rs1772611373, rs1772638226	RCV001784970 RCV001543362 RCV001733641 RCV001784971 RCV002290870 RCV002471515 RCV005356245 RCV000778788 RCV003387668 RCV005250319 RCV000022972 RCV000022973 RCV000022974 RCV000680097 RCV000778787 RCV000850156 RCV000985128 RCV001089505 RCV001089506 RCV001257082 RCV001257083
Uterine corpus endometrial carcinoma	Pathogenic	rs144714933	RCV005931445

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Hepatocellular carcinoma	Conflicting classifications of pathogenicity	rs1276606764	RCV005930178
Lung cancer	Conflicting classifications of pathogenicity	rs144670908	RCV005921248
Malignant lymphoma, large B-cell, diffuse	Benign; Likely benign	rs440454, rs449643	RCV005915104 RCV005899067
Malignant tumor of esophagus	Benign	rs375693076	RCV005921257
Melanoma	Conflicting classifications of pathogenicity	rs144670908	RCV005921247
See cases	Conflicting classifications of pathogenicity	rs148221996	RCV003128561
Thyroid cancer, nonmedullary, 1	Uncertain significance; Likely benign	rs775680687, rs750646943	RCV005926752 RCV005936620
Uveal melanoma	Benign; Likely benign	rs449643	RCV005899066