RNF7

ring finger protein 7, the group of Ring finger proteins

Basic information

Region (hg38): 3:141738249-141747560

Links

ENSG00000114125

∙ NCBI:9616 ∙ OMIM:603863 ∙ HGNC:10070 ∙ Uniprot:Q9UBF6 ∙ 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 RNF7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF7 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			2 clinvar			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in RNF7

This is a list of pathogenic ClinVar variants found in the RNF7 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-141738370-C-G		not specified	Uncertain significance (Dec 16, 2022)	2388085
3-141738375-G-A		not specified	Uncertain significance (Mar 21, 2023)	2527420

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF7	protein_coding	protein_coding	ENST00000273480	3	9357

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0329	0.831	125739	0	7	125746	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.56	28	62.9	0.445	0.00000293	751
Missense in Polyphen		2	18.237	0.10967		237
Synonymous	0.125	21	21.7	0.966	0.00000107	183
Loss of Function	1.17	3	6.14	0.488	2.62e-7	66

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000295	0.0000295
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000666	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Probable component of the SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complex which mediates the ubiquitination and subsequent proteasomal degradation of target proteins involved in cell cycle progression, signal transduction and transcription (PubMed:10851089). CRLs complexes and ARIH1 collaborate in tandem to mediate ubiquitination of target proteins, ARIH1 mediating addition of the first ubiquitin on CRLs targets (By similarity). Through the RING-type zinc finger, seems to recruit the E2 ubiquitination enzyme to the complex and brings it into close proximity to the substrate. Promotes the neddylation of CUL5 via its interaction with UBE2F. May play a role in protecting cells from apoptosis induced by redox agents. {ECO:0000250|UniProtKB:P62877, ECO:0000269|PubMed:10851089}.;
Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Apoptosis-related network due to altered Notch3 in ovarian cancer;Post-translational protein modification;Metabolism of proteins;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Neddylation (Consensus)

Recessive Scores

pRec: 0.124

Intolerance Scores

loftool: 0.622
rvis_EVS: 0.04
rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

pHI: 0.150
hipred: Y
hipred_score: 0.765
ghis: 0.633

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.781

Mouse Genome Informatics

Gene name: Rnf7
Phenotype: growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); neoplasm; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; skeleton phenotype;

Gene ontology

Biological process: ubiquitin-dependent protein catabolic process;protein ubiquitination;SCF-dependent proteasomal ubiquitin-dependent protein catabolic process;post-translational protein modification;protein neddylation;response to redox state
Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;cullin-RING ubiquitin ligase complex;Cul2-RING ubiquitin ligase complex;Cul3-RING ubiquitin ligase complex;Cul5-RING ubiquitin ligase complex;Cul7-RING ubiquitin ligase complex;nuclear SCF ubiquitin ligase complex;Cul4-RING E3 ubiquitin ligase complex
Molecular function: copper ion binding;protein binding;zinc ion binding;NEDD8 transferase activity;ubiquitin protein ligase activity;cullin family protein binding