RNF130

ring finger protein 130, the group of MicroRNA protein coding host genes|Ring finger proteins

Basic information

Region (hg38): 5:179911650-180072113

Links

ENSG00000113269 ∙ NCBI:55819 ∙ OMIM:619163 ∙ HGNC:18280 ∙ Uniprot:Q86XS8 ∙ 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 RNF130 gene.

• Inborn genetic diseases (19 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF130 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					1	1
missense			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	1

Variants in RNF130

This is a list of pathogenic ClinVar variants found in the RNF130 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-179963537-C-A		not specified	Uncertain significance (May 26, 2023)
5-179966851-C-T		not specified	Uncertain significance (Jan 26, 2023)
5-179966867-T-C			Benign (Feb 25, 2018)
5-179966868-G-A		not specified	Uncertain significance (Aug 15, 2023)
5-179966880-G-A		not specified	Uncertain significance (Jun 02, 2023)
5-179966896-G-C		not specified	Uncertain significance (Aug 11, 2022)
5-179966914-C-T		not specified	Likely benign (Aug 10, 2021)
5-179970459-C-T		not specified	Uncertain significance (Oct 27, 2023)
5-179978222-C-T		not specified	Uncertain significance (Dec 20, 2021)
5-179978226-A-C		not specified	Uncertain significance (Dec 12, 2023)
5-179980199-C-T		not specified	Uncertain significance (May 04, 2023)
5-180013074-C-T		not specified	Uncertain significance (May 23, 2023)
5-180013194-G-A		not specified	Uncertain significance (Apr 06, 2023)
5-180040519-T-C		not specified	Uncertain significance (Oct 06, 2021)
5-180040533-C-T		not specified	Uncertain significance (May 03, 2023)
5-180040606-C-T		not specified	Uncertain significance (Jul 12, 2023)
5-180071461-T-C		not specified	Uncertain significance (Dec 20, 2023)
5-180071545-G-C		not specified	Uncertain significance (Nov 05, 2021)
5-180071626-C-T		not specified	Uncertain significance (Mar 07, 2024)
5-180071634-C-G		not specified	Uncertain significance (Aug 17, 2021)
5-180071657-C-A		not specified	Uncertain significance (Mar 17, 2023)
5-180071662-G-A		not specified	Uncertain significance (Apr 17, 2023)
5-180071669-G-T		not specified	Uncertain significance (Dec 18, 2023)
5-180071678-G-A		not specified	Uncertain significance (Nov 18, 2022)
5-180071695-C-T		not specified	Uncertain significance (Feb 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF130	protein_coding	protein_coding	ENST00000521389	9	160468

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000303	0.988	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.77	159	235	0.676	0.0000130	2702
Missense in Polyphen		43	75.645	0.56844		841
Synonymous	1.40	69	85.5	0.807	0.00000489	810
Loss of Function	2.22	9	19.6	0.459	0.00000113	219

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000187	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000534	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May have a role during the programmed cell death of hematopoietic cells (By similarity). Acts as an E3 ubiquitin- protein ligase. {ECO:0000250, ECO:0000269|PubMed:16549277}.
• Pathway: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.300

Intolerance Scores

• loftool: 0.212
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.91

Haploinsufficiency Scores

• pHI: 0.816
• hipred: Y
• hipred_score: 0.765
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.840

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf130

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;apoptotic process;programmed cell death;protein ubiquitination
• Cellular component: cytoplasm;integral component of membrane
• Molecular function: ubiquitin-protein transferase activity;metal ion binding;ubiquitin protein ligase activity