RNF19B

ring finger protein 19B, the group of Ring finger proteins|RBR E3 ubiquitin ligases

Basic information

Region (hg38): 1:32936445-32964809

Previous symbols: [ "IBRDC3" ]

Links

ENSG00000116514 ∙ NCBI:127544 ∙ OMIM:610872 ∙ HGNC:26886 ∙ Uniprot:Q6ZMZ0 ∙ 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 RNF19B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF19B 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			53	1		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	53	1	0

Variants in RNF19B

This is a list of pathogenic ClinVar variants found in the RNF19B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-32936853-C-T		not specified	Uncertain significance (Dec 16, 2022)
1-32936868-G-A		not specified	Uncertain significance (Apr 23, 2024)
1-32936872-C-T		not specified	Uncertain significance (Jan 01, 2025)
1-32936891-G-T		not specified	Uncertain significance (Jan 02, 2024)
1-32936930-G-A		not specified	Uncertain significance (Jan 29, 2025)
1-32936940-G-A		not specified	Uncertain significance (Dec 19, 2023)
1-32936951-C-A		not specified	Uncertain significance (Jan 22, 2025)
1-32936963-G-A		not specified	Uncertain significance (Oct 29, 2024)
1-32937006-G-C		not specified	Uncertain significance (Apr 25, 2022)
1-32937009-C-T		not specified	Uncertain significance (Aug 01, 2024)
1-32937014-C-T		not specified	Uncertain significance (Sep 08, 2024)
1-32937065-C-G		not specified	Uncertain significance (Apr 18, 2024)
1-32937098-G-T		not specified	Uncertain significance (Sep 17, 2021)
1-32937117-C-T		not specified	Uncertain significance (May 17, 2023)
1-32937120-C-T		not specified	Uncertain significance (Apr 06, 2024)
1-32937182-G-A		not specified	Uncertain significance (Feb 15, 2023)
1-32937210-G-A		not specified	Uncertain significance (Oct 04, 2022)
1-32938439-G-T		not specified	Uncertain significance (Sep 20, 2023)
1-32938442-C-T		not specified	Uncertain significance (Nov 14, 2024)
1-32938463-A-G		not specified	Uncertain significance (Mar 18, 2024)
1-32942286-C-T		not specified	Uncertain significance (Dec 06, 2024)
1-32942297-G-A		not specified	Uncertain significance (Dec 27, 2022)
1-32942386-C-G		not specified	Uncertain significance (Apr 28, 2022)
1-32944087-C-T		not specified	Uncertain significance (Dec 11, 2024)
1-32945574-T-C		not specified	Uncertain significance (Aug 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF19B	protein_coding	protein_coding	ENST00000373456	9	28241

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.924	0.0763	125715	0	33	125748	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.27	233	353	0.660	0.0000183	4751
Missense in Polyphen		76	157.14	0.48364		1866
Synonymous	-0.234	135	132	1.03	0.00000740	1476
Loss of Function	3.98	4	25.9	0.155	0.00000127	331

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000255	0.000255
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from E2 ubiquitin-conjugating enzymes UBE2L3 and UBE2L6 in the form of a thioester and then directly transfers the ubiquitin to targeted substrates, such as UCKL1 (PubMed:16709802, PubMed:27485036). Involved in the cytolytic activity of natural killer cells and cytotoxic T-cells (PubMed:10438909). Protects against staurosporin-induced cell death (PubMed:27485036). {ECO:0000269|PubMed:10438909, ECO:0000269|PubMed:16709802, ECO:0000269|PubMed:27485036}.
• Pathway: Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.0930

Intolerance Scores

• loftool: 0.382
• rvis_EVS: -0.78
• rvis_percentile_EVS: 12.77

Haploinsufficiency Scores

• pHI: 0.492
• hipred: Y
• hipred_score: 0.853
• ghis: 0.587

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.732

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf19b
• Phenotype: hematopoietic system phenotype; neoplasm; immune system phenotype

Gene ontology

• Biological process: protein polyubiquitination;adaptive immune response;ubiquitin-dependent protein catabolic process;positive regulation of proteasomal ubiquitin-dependent protein catabolic process
• Cellular component: ubiquitin ligase complex;cytoplasm;endoplasmic reticulum membrane;cytosol;integral component of membrane;cytolytic granule
• Molecular function: ubiquitin-protein transferase activity;protein binding;ubiquitin conjugating enzyme binding;metal ion binding;ubiquitin protein ligase activity