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

Summary

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: mouse all
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Genomic context

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_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-16314 (e-PCR)
- UniSTS:65600

RH70616 (e-PCR)
- UniSTS:32381

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

EC 3.6.4.13

XP_011513117.1

EC 3.6.4.13

XP_047275215.1

EC 3.6.4.13

XP_047275216.1

EC 3.6.4.13

XP_054185828.1

EC 3.6.4.13

XP_054185829.1

EC 3.6.4.13

XP_054185830.1

EC 3.6.4.13

XP_054186311.1

EC 3.6.4.13

XP_054186312.1

EC 3.6.4.13

XP_054186313.1

EC 3.6.4.13

XP_054186827.1

EC 3.6.4.13

XP_054186828.1

EC 3.6.4.13

XP_054186829.1

EC 3.6.4.13

XP_054187089.1

EC 3.6.4.13

XP_054187090.1

EC 3.6.4.13

XP_054187091.1

EC 3.6.4.13

XP_054187350.1

EC 3.6.4.13

XP_054187351.1

EC 3.6.4.13

XP_054187352.1

EC 3.6.4.13

XP_054212214.1

EC 3.6.4.13

XP_054212215.1

EC 3.6.4.13

XP_054212216.1

EC 3.6.4.13

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

NG_032652.1 RefSeqGene

Range

5372..15948

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

31959175..31969751

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

H7C5N0

Related

ENSP00000420332.2, ENST00000483553.6
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

NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

Range

3436602..3447178

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A8V8TLC0
XM_054329854.1 → XP_054185829.1 superkiller complex protein 2 isoform X2

UniProtKB/TrEMBL

H7C5N0
XM_054329855.1 → XP_054185830.1 superkiller complex protein 2 isoform X3