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	9652
Gene name	SKI3 subunit of superkiller complex
Gene symbol	SKIC3
Synonyms (NCBI Gene)	KIAA0372Ski3THESTTC37
Chromosome	5
Chromosome location	5q15

Show/Hide all (23)

SNP ID	Visualize variation	Clinical significance	Consequence
rs116690692	T>C,G	Likely-benign, benign-likely-benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant, genic downstream transcript variant
rs138144509	C>A	Likely-pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs140800288	G>A	Likely-pathogenic	Stop gained, coding sequence variant, genic downstream transcript variant
rs143346257	C>G	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant, non coding transcript variant
rs370373017	C>A,G,T	Pathogenic	Splice donor variant, genic downstream transcript variant
rs376083373	T>C	Conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, coding sequence variant, synonymous variant
rs387907147	G>A	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs387907148	G>A	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained
rs534237033	C>T	Pathogenic	Coding sequence variant, intron variant, stop gained
rs570910902	C>T	Likely-pathogenic	Splice donor variant
rs746874042	AAAAA>-,AAAA	Pathogenic	Intron variant
rs752052886	A>-	Likely-pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs771031428	->T	Pathogenic	Genic downstream transcript variant, coding sequence variant, frameshift variant
rs774405964	T>-	Pathogenic	Coding sequence variant, frameshift variant, genic downstream transcript variant
rs776321294	G>A,C	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant, missense variant
rs1060499527	C>-	Pathogenic	Splice donor variant, coding sequence variant, non coding transcript variant
rs1060499528	C>G	Pathogenic	Splice donor variant
rs1269943135	G>A	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant
rs1554050112	A>-	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant
rs1580193628	CT>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1580193741	G>A	Likely-pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1582849711	->GT	Likely-pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant
rs1582849807	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant

Show/Hide all (44)

miRTarBase ID	miRNA	Experiments	Reference
MIRT016132	hsa-miR-421	Sequencing	20371350
MIRT020839	hsa-miR-155-5p	Proteomics	18668040
MIRT023848	hsa-miR-1-3p	Proteomics	18668040
MIRT049507	hsa-miR-92a-3p	CLASH	23622248
MIRT038611	hsa-miR-186-3p	CLASH	23622248
MIRT619481	hsa-miR-3617-5p	HITS-CLIP	23824327
MIRT619480	hsa-miR-641	HITS-CLIP	23824327
MIRT038611	hsa-miR-186-3p	HITS-CLIP	23824327
MIRT619479	hsa-miR-3190-5p	HITS-CLIP	23824327
MIRT619478	hsa-miR-3176	HITS-CLIP	23824327
MIRT619477	hsa-miR-3922-3p	HITS-CLIP	23824327
MIRT565185	hsa-miR-4475	PAR-CLIP	20371350
MIRT565180	hsa-miR-101-3p	PAR-CLIP	20371350
MIRT565184	hsa-miR-144-3p	PAR-CLIP	20371350
MIRT565183	hsa-miR-6504-3p	PAR-CLIP	20371350
MIRT565182	hsa-miR-545-5p	PAR-CLIP	20371350
MIRT565181	hsa-miR-6892-5p	PAR-CLIP	20371350
MIRT565180	hsa-miR-101-3p	PAR-CLIP	20371350
MIRT565179	hsa-miR-582-5p	PAR-CLIP	20371350
MIRT565178	hsa-miR-5701	PAR-CLIP	20371350
MIRT565177	hsa-miR-4482-3p	PAR-CLIP	20371350
MIRT439381	hsa-miR-377-5p	HITS-CLIP	24374217
MIRT439379	hsa-miR-127-5p	HITS-CLIP	24374217
MIRT439380	hsa-miR-544a	HITS-CLIP	24374217
MIRT439381	hsa-miR-377-5p	HITS-CLIP	24374217
MIRT439379	hsa-miR-127-5p	HITS-CLIP	24374217
MIRT439380	hsa-miR-544a	HITS-CLIP	24374217
MIRT619481	hsa-miR-3617-5p	HITS-CLIP	23824327
MIRT619480	hsa-miR-641	HITS-CLIP	23824327
MIRT038611	hsa-miR-186-3p	HITS-CLIP	23824327
MIRT619479	hsa-miR-3190-5p	HITS-CLIP	23824327
MIRT619478	hsa-miR-3176	HITS-CLIP	23824327
MIRT619477	hsa-miR-3922-3p	HITS-CLIP	23824327
MIRT565185	hsa-miR-4475	PAR-CLIP	20371350
MIRT565180	hsa-miR-101-3p	PAR-CLIP	20371350
MIRT565184	hsa-miR-144-3p	PAR-CLIP	20371350
MIRT565183	hsa-miR-6504-3p	PAR-CLIP	20371350
MIRT565182	hsa-miR-545-5p	PAR-CLIP	20371350
MIRT565181	hsa-miR-6892-5p	PAR-CLIP	20371350
MIRT565180	hsa-miR-101-3p	PAR-CLIP	20371350
MIRT565179	hsa-miR-582-5p	PAR-CLIP	20371350
MIRT565178	hsa-miR-5701	PAR-CLIP	20371350
MIRT565177	hsa-miR-4482-3p	PAR-CLIP	20371350
MIRT2138682	hsa-miR-1264	CLIP-seq

Show/Hide all (16)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000791	Component	Euchromatin	IDA	16024656
GO:0000956	Process	Nuclear-transcribed mRNA catabolic process	IBA
GO:0005515	Function	Protein binding	IPI	16024656
GO:0005634	Component	Nucleus	IDA	16024656
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IDA	16024656
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	TAS
GO:0006401	Process	RNA catabolic process	IEA
GO:0055087	Component	Ski complex	IBA
GO:0055087	Component	Ski complex	IDA	16024656, 32006463, 35120588
GO:0055087	Component	Ski complex	IEA
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
614589	23639	ENSG00000198677

Q6PGP7

Protein name

Superkiller complex protein 3 (Ski3) (Tetratricopeptide repeat protein 37) (TPR repeat protein 37) (Tricho-hepatic-enteric syndrome protein) (Thespin)

Protein function

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 extraction from 80

PDB

7QDR , 7QDS , 7QDY , 7QDZ , 9G8O , 9G8Q , 9G8R

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF13181	TPR_8	40 → 73	Tetratricopeptide repeat	Repeat
PF13432	TPR_16	391 → 450		Family
PF13432	TPR_16	568 → 632		Family
PF13181	TPR_8	861 → 894	Tetratricopeptide repeat	Repeat
PF13181	TPR_8	1400 → 1433	Tetratricopeptide repeat	Repeat

Tissue specificity

TISSUE SPECIFICITY: Widely expressed with the highest levels observed in vascular tissues, lymph node, pituitary, lung and intestine. Not expressed in the liver. {ECO:0000269|PubMed:21120949}.

Sequence

MSSKEVKTALKSARDAIRNKEYKEALKHCKTVLKQEKNNYNAWVFIGVAAAELEQPDQAQ
SAYKKAAELEPDQLLAWQGLANLYEKYNHINAKDDLPGVYQKLLDLYESVDKQKWCDVCK
KLVDLYYQEKKHLEVARTWHKLIKTRQEQGAENEELHQLWRKLTQFLAESTEDQNNETQQ
LLFTAFENALGLSDKIPSEDHQVLYRHFIQSLSKFPHESARLKKACEGMINIYPTVQYPL
EVLCLHLIESGNLTDEGQQYCCRLVEMDSKSGPGLIGLGIKALQDKKYEDAVRNLTEGLK
ESPVCTSGWYHLAEAQVKMHRPKEAVLSCSQALKIVDNLGASGNSLYQRNLCLHLKAEAL
IKLSDYDSSEEAIRTLDQISDADNIPGLLVLKSLAYRNKGSFDEAAKIMEDLLSSYPDLA
EVHALEALIHFTKKDYLQAEKCFQRALEKDTEVAEYHYQLGLTYWFMGEETRKDKTKALT
HFLKAARLDTYMGKVFCYLGHYYRDVVGDKNRARGCYRKAFELDDTDAESGAAAVDLSVE
LEDMEMALAILTTVTQKASAGTAKWAWLRRGLYYLKAGQHSQAVADLQAALRADPKDFNC
WESLGEAYLSRGGYTTALKSFTKASELNPESIYSVFKVAAIQQILGKYKEAVAQYQMIIK
KKEDYVPALKGLGECHLMMAKAALVDYLDGKAVDYIEKALEYFTCALQHRADVSCLWKLA
GDACTCLYAVAPSKVNVHVLGVLLGQKEGKQVLKKNELLHLGGRCYGRALKLMSTSNTWC
DLGINYYRQAQHLAETGSNMNDLKELLEKSLHCLKKAVRLDSNNHLYWNALGVVACYSGI
GNYALAQHCFIKSIQSEQINAVAWTNLGVLYLTNENIEQAHEAFKMAQSLDPSYLMCWIG
QALIAEAVGSYDTMDLFRHTTELNMHTEGALGYAYWVCTTLQDKSNRETELYQYNILQMN
AIPAAQVILNKYVERIQNYAPAFTMLGYLNEHLQLKKEAANAYQRAILLLQTAEDQDTYN
VAIRNYGRLLCSTGEYDKAIQAFKSTPLEVLEDIIGFALALFMKGLYKESSKAYERALSI
VESEQDKAHILTALAITEYKQGKTDVAKTLLFKCSILKEPTTESLQALCALGLAMQDATL
SKAALNELLKHIKHKDSNYQRCLLTSAIYALQGRSVAVQKQISKAVHSNPGDPALWSLLS
RVVAQYAQRNAKGGVVAGNVAHILDSNHGKKALLYTAVNQLAMGSSSAEDEKNTALKTIQ
KAALLSPGDPAIWAGLMAACHADDKLALVNNTQPKRIDLYLALLSAVSASIKDEKFFENY
NQSLEKWSLSQAVTGLIDTGRISEAETLCTKNLKSNPDQPAVILLLRQVQCKPLLESQKP
LPDAVLEELQKTVMSNSTSVPAWQWLAHVYQSQGMMRAAEMCYRKSLQLASQRGSWSGKL
SSLLRLALLALKVCMANISNDHWPSLVQEATTEALKLCFCPLAVLLQALLQFKRKMGARE
TRRLLERVVYQPGYPKSIASTARWYLLRHLYAKDDYELIDVLVNNAKTHGDTRALELNQR
LSSQ

Sequence length

1564

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 (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Inherited Immunodeficiency Diseases	Likely pathogenic; Pathogenic	rs140800288, rs570910902	RCV001027640 RCV001027639	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Malignant tumor of urinary bladder	Pathogenic	rs768215813	RCV005925363	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SKIC3-related disorder	Pathogenic; Likely pathogenic	rs1438402975, rs2112320552, rs776321294	RCV004754882 RCV003397532 RCV003420199	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Thyroid cancer, nonmedullary, 1	Likely pathogenic	rs771111803	RCV005934832	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Trichohepatoenteric syndrome	Likely pathogenic; Pathogenic	rs2112344385, rs769075304, rs2112260281, rs1321345597, rs763823697, rs2530762171, rs1389762829, rs2530717673, rs750568866, rs1580193741	RCV001553699 RCV003317528 RCV003226504 RCV004801110 RCV003492752 RCV002470094 RCV003226569 RCV003231044 RCV005407186 RCV000825551	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Trichohepatoenteric syndrome 1	Likely pathogenic; Pathogenic	rs766378178, rs769075304, rs373796916, rs2112320552, rs2112237964, rs2112308448, rs755681347, rs2112308481, rs763823697, rs534237033, rs1438402975, rs2530746798, rs751870750, rs2530727382, rs1158743738 View all (17 more)	RCV001783926 RCV001805759 RCV002497874 RCV002210927 RCV002210928 RCV002246795 RCV002250956 RCV002251072 RCV002290871 RCV000176881 RCV004999777 RCV003132990 RCV003485868 RCV003445356 RCV004787068 RCV003990628 RCV004555823 RCV004566645 RCV000024231 RCV000024232 RCV000024233 RCV000024234 RCV000024235 RCV000024236 RCV000680169 RCV000985205 RCV000991433 RCV001007869 RCV005225200 RCV002489529 RCV002497347 RCV001197818	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (19)

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.
Acute myeloid leukemia	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Adrenocortical carcinoma, hereditary	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Chronic lymphocytic leukemia/small lymphocytic lymphoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign; Likely benign; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign; Likely benign; Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MALIGNANT URINARY SYSTEM NEOPLASM	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Prostate cancer	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Uncertain significance; Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

SKIC3 (SKI3 subunit of superkiller complex)