GeneBe

SKIC8

SKI8 subunit of superkiller complex, the group of Paf1/RNA polymerase II complex |SKI complex subunits|WD repeat domain containing

Basic information

Region (hg38): 15:78277835-78299703

Previous symbols: [ "WDR61" ]

Links

ENSG00000140395 ∙ NCBI:80349 ∙ OMIM:609540 ∙ HGNC:30300 ∙ Uniprot:Q9GZS3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SKIC8 gene.

  • not_specified (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SKIC8 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000025234.3. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
0
missense
19
clinvar
 19
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 19 0 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SKIC8protein_codingprotein_codingENST00000267973 1021960
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.004800.9901257350131257480.0000517
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.95961670.5750.000008392009
Missense in Polyphen2050.6880.39457630
Synonymous0.7385461.40.8800.00000330579
Loss of Function2.43718.20.3857.71e-7207

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00005790.0000579
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.00004620.0000462
European (Non-Finnish)0.00007930.0000791
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non- phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of KMT2A/MLL1; it promotes leukemogenesis through association with KMT2A/MLL1-rearranged oncoproteins, such as KMT2A/MLL1-MLLT3/AF9 and KMT2A/MLL1-MLLT1/ENL. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors. In case of infection by influenza A strain H3N2, PAF1C associates with viral NS1 protein, thereby regulating gene transcription. Required for mono- and trimethylation on histone H3 'Lys-4' (H3K4me3), dimethylation on histone H3 'Lys-79' (H3K4me3). Required for Hox gene transcription. Component of the SKI complex which is thought to be involved in exosome-mediated RNA decay and associates with transcriptionally active genes in a manner dependent on PAF1C. {ECO:0000269|PubMed:16024656, ECO:0000269|PubMed:16307923, ECO:0000269|PubMed:19952111, ECO:0000269|PubMed:20178742}.;
Pathway
RNA degradation - Homo sapiens (human);Gene expression (Transcription);RNA Polymerase II Pre-transcription Events;Post-translational protein modification;Formation of RNA Pol II elongation complex ;Metabolism of proteins;RNA Polymerase II Transcription;Metabolism of RNA;RNA Polymerase II Transcription Elongation;Protein ubiquitination;mRNA decay by 3, to 5, exoribonuclease;Deadenylation-dependent mRNA decay;E3 ubiquitin ligases ubiquitinate target proteins (Consensus)

Recessive Scores

pRec
0.135

Intolerance Scores

loftool
0.418
rvis_EVS
-0.43
rvis_percentile_EVS
25.15

Haploinsufficiency Scores

pHI
0.422
hipred
Y
hipred_score
0.669
ghis
0.691

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.970

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Wdr61
Phenotype

Gene ontology

Biological process
transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;Wnt signaling pathway;protein ubiquitination;positive regulation of transcription elongation from RNA polymerase II promoter;exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay;negative regulation of myeloid cell differentiation;positive regulation of transcription by RNA polymerase II;positive regulation of histone H3-K4 methylation;histone H3-K4 trimethylation;positive regulation of histone H3-K79 methylation
Cellular component
nucleus;nucleoplasm;cytoplasm;cytosol;Cdc73/Paf1 complex;transcriptionally active chromatin;Ski complex
Molecular function
protein binding