Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	6499
Gene name	SKI2 subunit of superkiller complex
Gene symbol	SKIC2
Synonyms (NCBI Gene)	170ADDX13HLPSKI2SKI2WSKIV2SKIV2LSKIV2L1THES2
Chromosome	6
Chromosome location	6p21.33

Show/Hide all (10)

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

Show/Hide all (7)

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

Show/Hide all (21)

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

MIM	HGNC	e!Ensembl
600478	10898	ENSG00000204351

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

Interactions

View interactions

	KEGG		Reactome
	RNA degradation		mRNA decay by 3' to 5' exoribonuclease

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Gastric cancer	Likely pathogenic	rs762751779	RCV005912589	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Immunodeficiency 57	Pathogenic	rs767084483	RCV004999788	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Ovarian serous cystadenocarcinoma	Likely pathogenic	rs1419680561, rs1375849231	RCV005934624 RCV005936616	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SKIC2-related disorder	Pathogenic; Likely pathogenic	rs138923214, rs1353707093, rs200818962, rs2482913862, rs2482998760, rs751026211	RCV003956370 RCV003407950 RCV004752805 RCV003429065 RCV003911543 RCV003390696	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Trichohepatoenteric syndrome	Pathogenic; Likely pathogenic	rs138923214, rs759511516, rs200271795, rs1772636752, rs2483002672, rs1244156082, rs899709021, rs377014444, rs2482913862	RCV003155429 RCV003155397 RCV001844644 RCV002240109 RCV002470082 RCV003123466 RCV003155841 RCV003226784 RCV006269838	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Trichohepatoenteric syndrome 2	Pathogenic; Likely pathogenic	rs138923214, rs759511516, rs1772848223, rs750724648, rs1772679892, rs2482893792, rs1475859257, rs200818962, rs144714933, rs969421193, rs751026211, rs281875237, rs1562659544, rs781763471, rs768503878 View all (6 more)	RCV001784970 RCV001543362 RCV001733641 RCV001784971 RCV002290870 RCV002471515 RCV005356245 RCV000778788 RCV003387668 RCV005250319 RCV000022972 RCV000022973 RCV000022974 RCV000680097 RCV000778787 RCV000850156 RCV000985128 RCV001089505 RCV001089506 RCV001257082 RCV001257083	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Uterine corpus endometrial carcinoma	Pathogenic	rs144714933	RCV005931445	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (20)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
ATROPHIC MACULAR DEGENERATION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CANDIDEMIA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEGENERATION OF MACULA AND POSTERIOR POLE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLAUCOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IMMUNODEFICIENCY 57 WITH AUTOINFLAMMATION	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MACULAR DEGENERATION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MIGRAINE DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MOUTH NEOPLASM	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-ALCOHOLIC FATTY LIVER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSORIATIC ARTHRITIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Uncertain significance; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WET MACULAR DEGENERATION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

SKIC2 (SKI2 subunit of superkiller complex)