RNF19A

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

Basic information

Region (hg38): 8:100257060-100336218

Previous symbols: [ "RNF19" ]

Links

ENSG00000034677 ∙ NCBI:25897 ∙ OMIM:607119 ∙ HGNC:13432 ∙ Uniprot:Q9NV58 ∙ 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 RNF19A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF19A 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			24	2		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	1

Variants in RNF19A

This is a list of pathogenic ClinVar variants found in the RNF19A region.

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

Position	Type	Phenotype	Significance	ClinVar
8-100258611-T-C		not specified	Uncertain significance (Oct 10, 2023)
8-100258668-T-C		not specified	Likely benign (Apr 12, 2022)
8-100258788-T-A		not specified	Uncertain significance (Mar 24, 2023)
8-100258798-T-C		not specified	Uncertain significance (May 03, 2023)
8-100258815-C-T		not specified	Uncertain significance (Oct 06, 2022)
8-100258942-G-C		not specified	Uncertain significance (Jun 29, 2023)
8-100258986-T-C		not specified	Uncertain significance (Mar 20, 2023)
8-100259007-G-A		not specified	Uncertain significance (Oct 02, 2023)
8-100259013-T-C		not specified	Uncertain significance (Dec 20, 2023)
8-100259079-T-G		not specified	Uncertain significance (Mar 28, 2024)
8-100259131-C-T		not specified	Uncertain significance (Dec 28, 2022)
8-100259143-T-C		not specified	Uncertain significance (Jun 29, 2023)
8-100259167-C-T		not specified	Uncertain significance (May 30, 2023)
8-100259858-C-G		not specified	Uncertain significance (Apr 06, 2023)
8-100259950-C-T		not specified	Uncertain significance (Oct 02, 2023)
8-100261561-T-C		not specified	Uncertain significance (Nov 07, 2022)
8-100261584-G-A		not specified	Uncertain significance (Mar 07, 2023)
8-100264767-C-T		not specified	Uncertain significance (Nov 19, 2022)
8-100264775-C-T			Likely benign (Apr 01, 2023)
8-100274988-G-A		not specified	Uncertain significance (Aug 19, 2023)
8-100275077-G-C		not specified	Uncertain significance (Apr 06, 2024)
8-100275108-C-T		not specified	Uncertain significance (Jun 17, 2024)
8-100287529-A-T		not specified	Uncertain significance (Dec 20, 2023)
8-100287584-C-T			Benign (Mar 29, 2018)
8-100287610-G-C		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF19A	protein_coding	protein_coding	ENST00000519449	9	79159

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0253	0.975	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.38	322	467	0.690	0.0000245	5547
Missense in Polyphen		77	167.46	0.45981		1918
Synonymous	-0.0636	158	157	1.01	0.00000799	1608
Loss of Function	4.00	10	35.9	0.279	0.00000226	421

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000304	0.000304
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000176	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.000233	0.000229
Other	0.000163	0.000163

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 SNCAIP or CASR. Specifically ubiquitinates pathogenic SOD1 variants, which leads to their proteasomal degradation and to neuronal protection. {ECO:0000269|PubMed:11237715, ECO:0000269|PubMed:12145308, ECO:0000269|PubMed:12750386, ECO:0000269|PubMed:15456787, ECO:0000269|PubMed:16513638}.
• Pathway: Parkin-Ubiquitin Proteasomal System pathway;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.0865
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.77

Haploinsufficiency Scores

• pHI: 0.319
• hipred: Y
• hipred_score: 0.708
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf19a
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); cellular phenotype

Gene ontology

• Biological process: protein polyubiquitination;microtubule cytoskeleton organization;ubiquitin-dependent protein catabolic process;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;regulation of protein catabolic process at postsynapse, modulating synaptic transmission
• Cellular component: ubiquitin ligase complex;cytoplasm;centrosome;cytosol;integral component of membrane;hippocampal mossy fiber to CA3 synapse;postsynapse;glutamatergic synapse
• Molecular function: ubiquitin-protein transferase activity;transcription factor binding;ubiquitin conjugating enzyme binding;metal ion binding;ubiquitin protein ligase activity