RNF152

protein-coding

ring finger protein 152, the group of Ring finger proteins

Gene summary

Enables small GTPase binding activity and ubiquitin protein ligase activity. Involved in several processes, including cellular response to amino acid starvation; negative regulation of TORC1 signaling; and protein ubiquitination. Located in lysosomal membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_173557.3

Inheritance

—

ClinVar variants

U:39B:1

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr18:61,808,067-61,894,247

External References & Databases

Ensembl (ENSG00000176641)

Transcript & Mutation Effects

hg38 • Region Span ~86.2 kb

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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 RNF152 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 38

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

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173557.3. 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		1
missense			38 clinvar			38
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	39	1	0	40

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 58 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173557.3	RefSeq	NP_775828.1	1	MANE Select
ENST00000312828.4	Ensembl	ENSP00000316628.3	1	MANE Select
ENST00000591306.5	Ensembl	ENSP00000466492.1	1	Standard
ENST00000873265.1	Ensembl	ENSP00000543324.1	1	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
rnf152	Danio rerio	Structure: neural tube Quality: decreased width abnormal

Gene / Model

Organism

Observed Phenotype

rnf152

Danio rerio

Structure: neural tube

Quality: decreased width

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

mTOR signaling pathway - Homo sapiens (human)
Post-translational protein modification
Metabolism of proteins
Protein ubiquitination
E3 ubiquitin ligases ubiquitinate target proteins

Biological Process

apoptotic process
positive regulation of autophagy
protein ubiquitination
cellular response to amino acid starvation
protein K63-linked ubiquitination

Molecular Function

ubiquitin-protein transferase activity
small GTPase binding
metal ion binding
ubiquitin protein ligase activity

Cellular Component

lysosome
lysosomal membrane
integral component of organelle membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000312828
Coding exons: 1
Length: 86185
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 11
Defined: 125741
p: 0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.648	116	137	0.844	0.00000919	1307
Missense (PolyPhen)		50	64.181	0.77905		592
Synonymous	0.715	55	62.2	0.885	0.00000450	437
Loss of Function	1.39	2	5.53	0.362	2.37e-7	61

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: E3 ubiquitin-protein ligase mediating 'Lys-63'-linked polyubiquitination of RRAGA in response to amino acid starvation. Thereby, regulates mTORC1 signaling and plays a role in the cellular response to amino acid availability (PubMed:25936802). Also mediates 'Lys-48'-linked polyubiquitination of target proteins and their subsequent targeting to the proteasome for degradation. Induces apoptosis when overexpressed (PubMed:21203937). {ECO:0000269|PubMed:21203937, ECO:0000269|PubMed:25936802}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.218
RVIS EVS: -0.09
RVIS percentile EVS: 46.74

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.906

Gene Damage Prediction

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