RNF152

ring finger protein 152, the group of Ring finger proteins

Basic information

Region (hg38): 18:61808067-61894247

Links

ENSG00000176641

∙ NCBI:220441 ∙ OMIM:616512 ∙ HGNC:26811 ∙ Uniprot:Q8N8N0 ∙ 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 RNF152 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF152 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						0
missense			16 clinvar			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in RNF152

This is a list of pathogenic ClinVar variants found in the RNF152 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Phenotype	Significance	ClinVar
18-61815932-C-T	not specified	Uncertain significance (Feb 12, 2024)	3155122
18-61815986-C-T	not specified	Uncertain significance (Feb 28, 2023)	2459544
18-61815992-G-A	not specified	Uncertain significance (Jul 14, 2022)	2301863
18-61815995-T-C	not specified	Uncertain significance (Oct 12, 2021)	2254538
18-61816039-A-G	not specified	Uncertain significance (Sep 16, 2021)	2408391
18-61816067-C-A	not specified	Uncertain significance (Apr 18, 2023)	2537768
18-61816102-A-G	not specified	Uncertain significance (Apr 18, 2023)	2537767
18-61816135-C-T	not specified	Uncertain significance (Aug 13, 2021)	2209946
18-61816157-G-T	not specified	Uncertain significance (Apr 07, 2023)	2534980
18-61816162-A-G	not specified	Uncertain significance (Jul 09, 2021)	2236006
18-61816190-T-C	not specified	Uncertain significance (Mar 07, 2024)	3155120
18-61816219-G-A	not specified	Uncertain significance (Apr 09, 2024)	3314761
18-61816251-G-A	EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)	2681520
18-61816268-C-T	not specified	Uncertain significance (Oct 26, 2021)	2366382
18-61816277-C-T	not specified	Uncertain significance (Dec 01, 2023)	3155119
18-61816298-C-T	not specified	Uncertain significance (Oct 06, 2023)	3155118
18-61816301-G-A	not specified	Uncertain significance (Sep 12, 2023)	2587948
18-61816400-G-A	not specified	Uncertain significance (Apr 17, 2023)	2561582
18-61816403-G-A	not specified	Uncertain significance (Apr 09, 2024)	3314762

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF152	protein_coding	protein_coding	ENST00000312828	1	86185

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.129	0.788	125730	0	11	125741	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.648	116	137	0.844	0.00000919	1307
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000163	0.000163
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

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}.;
Pathway: mTOR signaling pathway - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;Protein ubiquitination;E3 ubiquitin ligases ubiquitinate target proteins (Consensus)

Recessive Scores

pRec: 0.111

Intolerance Scores

loftool: 0.218
rvis_EVS: -0.09
rvis_percentile_EVS: 46.74

Haploinsufficiency Scores

pHI: 0.708
hipred: N
hipred_score: 0.383
ghis: 0.513

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.906

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Rnf152
Phenotype

Zebrafish Information Network

Gene name: rnf152
Affected structure: neural tube
Phenotype tag: abnormal
Phenotype quality: decreased width

Gene ontology

Biological process: apoptotic process;positive regulation of autophagy;protein ubiquitination;cellular response to amino acid starvation;protein K63-linked ubiquitination;protein K48-linked ubiquitination;negative regulation of TORC1 signaling
Cellular component: lysosome;lysosomal membrane;integral component of organelle membrane
Molecular function: ubiquitin-protein transferase activity;small GTPase binding;metal ion binding;ubiquitin protein ligase activity