RNF17
Basic information
Region (hg38): 13:24764168-24879921
Previous symbols: [ "TDRD4" ]
Links
Phenotypes
GenCC
Source:
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 RNF17 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 | 3 | |||||
missense | 57 | 67 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 1 | ||||
non coding | 1 | |||||
Total | 0 | 0 | 57 | 7 | 7 |
Variants in RNF17
This is a list of pathogenic ClinVar variants found in the RNF17 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
13-24764229-G-C | not specified | Uncertain significance (Jul 12, 2023) | ||
13-24764286-C-T | not specified | Uncertain significance (Jan 17, 2024) | ||
13-24764291-A-G | not specified | Uncertain significance (Jun 21, 2022) | ||
13-24767352-T-C | not specified | Uncertain significance (Nov 15, 2021) | ||
13-24774835-G-C | not specified | Uncertain significance (Apr 18, 2023) | ||
13-24774841-G-A | not specified | Uncertain significance (May 28, 2023) | ||
13-24778318-T-C | not specified | Uncertain significance (Nov 07, 2022) | ||
13-24778357-G-A | not specified | Likely benign (Sep 16, 2021) | ||
13-24779690-T-G | not specified | Uncertain significance (Aug 23, 2021) | ||
13-24781869-C-T | not specified | Uncertain significance (Mar 01, 2023) | ||
13-24781934-T-C | not specified | Likely benign (Nov 08, 2021) | ||
13-24788097-A-G | not specified | Uncertain significance (Jul 12, 2023) | ||
13-24788103-A-G | not specified | Uncertain significance (Jun 21, 2022) | ||
13-24788112-G-A | not specified | Uncertain significance (May 01, 2022) | ||
13-24789747-A-G | not specified | Uncertain significance (Sep 01, 2021) | ||
13-24789763-A-G | not specified | Uncertain significance (Apr 08, 2024) | ||
13-24793064-A-G | not specified | Uncertain significance (Oct 04, 2022) | ||
13-24793131-C-T | not specified | Uncertain significance (Jun 02, 2024) | ||
13-24793154-A-G | Benign (May 14, 2018) | |||
13-24793206-A-G | Benign (Feb 20, 2018) | |||
13-24793250-G-A | Benign (May 14, 2018) | |||
13-24793275-T-C | not specified | Uncertain significance (Nov 30, 2021) | ||
13-24793276-T-G | not specified | Uncertain significance (May 17, 2023) | ||
13-24793287-C-T | not specified | Uncertain significance (Mar 29, 2022) | ||
13-24793294-G-A | not specified | Uncertain significance (Dec 06, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RNF17 | protein_coding | protein_coding | ENST00000255324 | 35 | 115770 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 1.55e-12 | 122915 | 84 | 2729 | 125728 | 0.0112 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.77 | 679 | 822 | 0.826 | 0.0000396 | 10684 |
Missense in Polyphen | 188 | 300.45 | 0.62573 | 3963 | ||
Synonymous | 0.993 | 266 | 287 | 0.925 | 0.0000151 | 2911 |
Loss of Function | 8.37 | 3 | 87.5 | 0.0343 | 0.00000420 | 1174 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0289 | 0.0288 |
Ashkenazi Jewish | 0.00131 | 0.00129 |
East Asian | 0.0868 | 0.0861 |
Finnish | 0.00465 | 0.00458 |
European (Non-Finnish) | 0.000875 | 0.000862 |
Middle Eastern | 0.0868 | 0.0861 |
South Asian | 0.00316 | 0.00308 |
Other | 0.00694 | 0.00687 |
dbNSFP
Source:
- Function
- FUNCTION: Seems to be involved in regulation of transcriptional activity of MYC. In vitro, inhibits DNA-binding activity of Mad- MAX heterodimers. Can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the cytoplasm. May be involved in spermiogenesis (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- 0.183
- rvis_EVS
- 0.17
- rvis_percentile_EVS
- 65.05
Haploinsufficiency Scores
- pHI
- 0.265
- hipred
- N
- hipred_score
- 0.382
- ghis
- 0.402
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.558
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rnf17
- Phenotype
- reproductive system phenotype; endocrine/exocrine gland phenotype;
Gene ontology
- Biological process
- multicellular organism development;spermatid development
- Cellular component
- nucleus;cytoplasm
- Molecular function
- protein homodimerization activity;metal ion binding