RTF1
RTF1 homolog, Paf1/RNA polymerase II complex component, the group of Paf1/RNA polymerase II complex
Basic information
Region (hg38): 15:41408408-41483563
Previous symbols: [ "KIAA0252" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTF1 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 28 | 29 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 28 | 1 | 0 |
Variants in RTF1
This is a list of pathogenic ClinVar variants found in the RTF1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 15-41417141-G-C | not specified | Uncertain significance (Oct 07, 2024) | ||
| 15-41417144-C-T | not specified | Uncertain significance (Mar 02, 2023) | ||
| 15-41417183-G-A | not specified | Uncertain significance (Nov 08, 2024) | ||
| 15-41417185-G-T | not specified | Uncertain significance (Oct 25, 2023) | ||
| 15-41417189-A-G | not specified | Uncertain significance (Aug 08, 2022) | ||
| 15-41417197-A-G | not specified | Uncertain significance (Aug 12, 2021) | ||
| 15-41417210-G-T | not specified | Likely benign (Apr 07, 2023) | ||
| 15-41417212-C-T | not specified | Uncertain significance (Aug 12, 2021) | ||
| 15-41417225-G-C | not specified | Uncertain significance (Dec 21, 2024) | ||
| 15-41417225-G-T | not specified | Uncertain significance (Oct 05, 2023) | ||
| 15-41417234-C-A | not specified | Uncertain significance (Oct 07, 2024) | ||
| 15-41417260-G-A | not specified | Uncertain significance (Dec 08, 2023) | ||
| 15-41417291-G-C | not specified | Uncertain significance (Dec 14, 2024) | ||
| 15-41417299-G-C | not specified | Uncertain significance (Feb 12, 2024) | ||
| 15-41438391-C-G | not specified | Uncertain significance (Jan 18, 2025) | ||
| 15-41452968-T-C | not specified | Uncertain significance (Sep 20, 2023) | ||
| 15-41457784-G-C | not specified | Uncertain significance (Jan 18, 2025) | ||
| 15-41464871-A-C | not specified | Uncertain significance (Oct 08, 2024) | ||
| 15-41466162-C-T | not specified | Uncertain significance (Oct 21, 2024) | ||
| 15-41466163-G-A | not specified | Uncertain significance (Aug 16, 2022) | ||
| 15-41466175-G-A | not specified | Uncertain significance (Aug 10, 2023) | ||
| 15-41470365-G-A | not specified | Uncertain significance (Aug 14, 2023) | ||
| 15-41471269-A-G | not specified | Uncertain significance (Feb 28, 2023) | ||
| 15-41474620-G-A | not specified | Uncertain significance (Jan 16, 2025) | ||
| 15-41474626-G-C | not specified | Uncertain significance (Jul 14, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RTF1 | protein_coding | protein_coding | ENST00000389629 | 18 | 75156 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.00000429 | 125743 | 0 | 5 | 125748 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 4.59 | 109 | 351 | 0.310 | 0.0000204 | 4655 |
| Missense in Polyphen | 22 | 98.353 | 0.22368 | 1116 | ||
| Synonymous | 0.429 | 118 | 124 | 0.951 | 0.00000669 | 1291 |
| Loss of Function | 5.64 | 1 | 39.0 | 0.0256 | 0.00000204 | 517 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000992 | 0.0000992 |
| East Asian | 0.0000624 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.0000624 | 0.0000544 |
| South Asian | 0.0000406 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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. Binds single-stranded DNA. Required for maximal induction of heat-shock genes. Required for the trimethylation of histone H3 'Lys-4' (H3K4me3) on genes involved in stem cell pluripotency; this function is synergistic with CXXC1 indicative for an involvement of a SET1 complex (By similarity). {ECO:0000250, ECO:0000269|PubMed:19345177, ECO:0000269|PubMed:20178742}.;
- Pathway
- Endoderm Differentiation;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;RNA Polymerase II Transcription Elongation;Protein ubiquitination;E3 ubiquitin ligases ubiquitinate target proteins
(Consensus)
Recessive Scores
- pRec
- 0.142
Intolerance Scores
- loftool
- 0.0703
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.07
Haploinsufficiency Scores
- pHI
- 0.656
- hipred
- Y
- hipred_score
- 0.825
- ghis
- 0.670
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.871
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rtf1
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Zebrafish Information Network
- Gene name
- rtf1
- Affected structure
- cardiac muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- absent
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;endodermal cell fate commitment;blastocyst growth;transcription by RNA polymerase II;transcription elongation from RNA polymerase II promoter;Wnt signaling pathway;protein ubiquitination;stem cell population maintenance;positive regulation of transcription elongation from RNA polymerase II promoter;positive regulation of transcription by RNA polymerase II;positive regulation of histone H3-K4 methylation;histone H3-K4 trimethylation
- Cellular component
- nucleoplasm;nucleolus;Cdc73/Paf1 complex
- Molecular function
- single-stranded DNA binding;RNA binding;protein binding;RNA polymerase II C-terminal domain phosphoserine binding