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

ENSG00000132972 ∙ NCBI:56163 ∙ OMIM:605793 ∙ HGNC:10060 ∙ Uniprot:Q9BXT8 ∙ 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 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	1	3
missense			47	5	5	57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	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		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)
13-24793064-A-G		not specified	Uncertain significance (Oct 04, 2022)
13-24793131-C-T		not specified	Uncertain significance (Dec 07, 2021)
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)
13-24793338-A-G		not specified	Uncertain significance (Sep 06, 2022)

GnomAD

Source: gnomAD

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: 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

	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