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GeneBe

RNF17

ring finger protein 17, the group of Ring finger proteins|Tudor domain containing

Basic information

Region (hg38): 13:24764168-24879921

Previous symbols: [ "TDRD4" ]

Links

ENSG00000132972NCBI:56163OMIM:605793HGNC:10060Uniprot:Q9BXT8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNF17 gene.

  • Inborn genetic diseases (50 variants)
  • not provided (12 variants)

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
2
clinvar
1
clinvar
3
missense
47
clinvar
5
clinvar
5
clinvar
57
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
?
1
1
non coding
?
1
clinvar
1
Total 0 0 47 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 Inborn genetic diseases Uncertain significance (Jul 12, 2023)2597323
13-24764291-A-G Inborn genetic diseases Uncertain significance (Jun 21, 2022)2411100
13-24767352-T-C Inborn genetic diseases Uncertain significance (Nov 15, 2021)2261577
13-24774835-G-C Inborn genetic diseases Uncertain significance (Apr 18, 2023)2537552
13-24774841-G-A Inborn genetic diseases Uncertain significance (May 28, 2023)2517810
13-24778318-T-C Inborn genetic diseases Uncertain significance (Nov 07, 2022)2206819
13-24778357-G-A Inborn genetic diseases Likely benign (Sep 16, 2021)2365426
13-24779690-T-G Inborn genetic diseases Uncertain significance (Aug 23, 2021)2246874
13-24781869-C-T Inborn genetic diseases Uncertain significance (Mar 01, 2023)2491981
13-24781934-T-C Inborn genetic diseases Likely benign (Nov 08, 2021)2366913
13-24788097-A-G Inborn genetic diseases Uncertain significance (Jul 12, 2023)2611241
13-24788103-A-G Inborn genetic diseases Uncertain significance (Jun 21, 2022)2218516
13-24788112-G-A Inborn genetic diseases Uncertain significance (May 01, 2022)2353401
13-24789747-A-G Inborn genetic diseases Uncertain significance (Sep 01, 2021)2397244
13-24793064-A-G Inborn genetic diseases Uncertain significance (Oct 04, 2022)2401148
13-24793131-C-T Inborn genetic diseases Uncertain significance (Dec 07, 2021)2359105
13-24793154-A-G Benign (May 14, 2018)787941
13-24793206-A-G Benign (Feb 20, 2018)776785
13-24793250-G-A Benign (May 14, 2018)784268
13-24793275-T-C Inborn genetic diseases Uncertain significance (Nov 30, 2021)2262961
13-24793276-T-G Inborn genetic diseases Uncertain significance (May 17, 2023)2528582
13-24793287-C-T Inborn genetic diseases Uncertain significance (Mar 29, 2022)2386610
13-24793294-G-A Inborn genetic diseases Uncertain significance (Dec 06, 2022)2333092
13-24793338-A-G Inborn genetic diseases Uncertain significance (Sep 06, 2022)2310355
13-24796241-A-G Inborn genetic diseases Uncertain significance (Jul 25, 2023)2592994

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RNF17protein_codingprotein_codingENST00000255324 35115770
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.001.55e-121229158427291257280.0112
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.776798220.8260.000039610684
Missense in Polyphen188300.450.625733963
Synonymous0.9932662870.9250.00001512911
Loss of Function8.37387.50.03430.000004201174

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.02890.0288
Ashkenazi Jewish0.001310.00129
East Asian0.08680.0861
Finnish0.004650.00458
European (Non-Finnish)0.0008750.000862
Middle Eastern0.08680.0861
South Asian0.003160.00308
Other0.006940.00687

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

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