RNF17

protein-coding

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

Gene summary

This gene is similar to a mouse gene that encodes a testis-specific protein containing a RING finger domain. Alternatively spliced transcript variants encoding different isoforms have been found. [provided by RefSeq, May 2010]

Previous symbols:

TDRD4

MANE transcript

NM_031277.3

Inheritance

—

ClinVar variants

U:152B:21

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.03

Max pathogenic AF

—

Genomic locus

chr13:24,764,169-24,879,921

External References & Databases

Ensembl (ENSG00000132972)

Transcript & Mutation Effects

hg38 • Region Span ~115.8 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RNF17 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 157

not providedTotal: 12

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031277.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	3 clinvar	1 clinvar	5
missense			149 clinvar	12 clinvar	5 clinvar	166
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	152	15	6	173

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 23 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031277.3	RefSeq	NP_112567.2	35	MANE Select
ENST00000255324.10	Ensembl	ENSP00000255324.5	35	MANE Select
NM_001184993.2	RefSeq	NP_001171922.1	35	Standard
ENST00000255325.6	Ensembl	ENSP00000255325.6	15	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

multicellular organism development
spermatid development

Molecular Function

protein homodimerization activity
metal ion binding

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000255324
Coding exons: 35
Length: 115770
Individuals with no LoFs: 122915
Homozygous LoFs: 84
Heterozygous LoFs: 2729
Defined: 125728
p: 0.0112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.77	679	822	0.826	0.0000396	10684
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00095	0.00092	rare
Latino/Admixed American	0.028	0.027	notable
Ashkenazi Jewish	0.0013	0.0013	notable
East Asian	0.087	0.086	notable
Finnish	0.0046	0.0046	notable
European (Non-Finnish)	0.00087	0.00086	rare
South Asian	0.0032	0.0031	notable
Other	0.0069	0.0069	notable

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.558

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium