RLF
RLF zinc finger, the group of Zinc fingers C2H2-type
Basic information
Region (hg38): 1:40161386-40240921
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (38 variants)
- not provided (6 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RLF gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 3 | ||||
| missense | 37 | 1 | 3 | 41 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 37 | 1 | 6 |
Variants in RLF
This is a list of pathogenic ClinVar variants found in the RLF region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-40161409-G-A | Inborn genetic diseases | Uncertain significance (Dec 14, 2022) | ||
| 1-40161420-C-G | Inborn genetic diseases | Uncertain significance (Mar 01, 2023) | ||
| 1-40161422-C-T | Inborn genetic diseases | Uncertain significance (Nov 09, 2021) | ||
| 1-40161436-G-C | Inborn genetic diseases | Uncertain significance (Mar 23, 2022) | ||
| 1-40161455-C-T | Inborn genetic diseases | Uncertain significance (May 11, 2022) | ||
| 1-40161476-A-G | Inborn genetic diseases | Uncertain significance (Dec 21, 2022) | ||
| 1-40161588-A-C | Inborn genetic diseases | Uncertain significance (Aug 19, 2021) | ||
| 1-40161590-A-T | Inborn genetic diseases | Uncertain significance (Oct 26, 2022) | ||
| 1-40202468-T-A | Inborn genetic diseases | Uncertain significance (Jul 12, 2023) | ||
| 1-40202498-A-G | Inborn genetic diseases | Uncertain significance (Apr 13, 2023) | ||
| 1-40202572-A-G | Benign (Apr 04, 2018) | |||
| 1-40202583-C-G | Benign (Mar 29, 2018) | |||
| 1-40231591-G-A | Inborn genetic diseases | Uncertain significance (Nov 07, 2022) | ||
| 1-40231605-A-G | Inborn genetic diseases | Uncertain significance (Aug 02, 2021) | ||
| 1-40231648-T-C | Inborn genetic diseases | Uncertain significance (Jun 24, 2022) | ||
| 1-40235958-T-C | Inborn genetic diseases | Uncertain significance (Apr 06, 2022) | ||
| 1-40236014-C-G | Inborn genetic diseases | Uncertain significance (Sep 28, 2022) | ||
| 1-40236033-A-G | Inborn genetic diseases | Uncertain significance (Mar 11, 2022) | ||
| 1-40236038-C-G | Inborn genetic diseases | Uncertain significance (Jan 09, 2023) | ||
| 1-40236196-A-C | Inborn genetic diseases | Uncertain significance (Aug 12, 2021) | ||
| 1-40236291-A-G | Inborn genetic diseases | Uncertain significance (Jan 17, 2023) | ||
| 1-40236572-T-C | Inborn genetic diseases | Uncertain significance (Dec 21, 2022) | ||
| 1-40236638-C-G | Inborn genetic diseases | Uncertain significance (Jun 24, 2022) | ||
| 1-40236648-G-A | Inborn genetic diseases | Uncertain significance (Jun 29, 2023) | ||
| 1-40237158-A-G | Inborn genetic diseases | Uncertain significance (Jul 25, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RLF | protein_coding | protein_coding | ENST00000372771 | 8 | 79549 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 2.28e-12 | 125122 | 0 | 1 | 125123 | 0.00000400 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.46 | 669 | 973 | 0.688 | 0.0000471 | 12682 |
| Missense in Polyphen | 107 | 321.14 | 0.33319 | 4151 | ||
| Synonymous | -0.225 | 358 | 353 | 1.02 | 0.0000167 | 3482 |
| Loss of Function | 7.93 | 0 | 73.2 | 0.00 | 0.00000402 | 1024 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000619 | 0.0000619 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in transcriptional regulation.;
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- loftool
- 0.00696
- rvis_EVS
- 0.08
- rvis_percentile_EVS
- 59.19
Haploinsufficiency Scores
- pHI
- 0.537
- hipred
- Y
- hipred_score
- 0.725
- ghis
- 0.493
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.941
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rlf
- 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); growth/size/body region phenotype;
Gene ontology
- Biological process
- regulation of transcription, DNA-templated;DNA integration;regulation of DNA methylation;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;chromosome organization;histone H3-K4 monomethylation
- Cellular component
- nucleus
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;zinc ion binding