RNF144B

ring finger protein 144B, the group of Ring finger proteins|RBR E3 ubiquitin ligases

Basic information

Region (hg38): 6:18387350-18468870

Previous symbols: [ "IBRDC2" ]

Links

ENSG00000137393 ∙ NCBI:255488 ∙ OMIM:618869 ∙ HGNC:21578 ∙ Uniprot:Q7Z419 ∙ 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 RNF144B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF144B 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	2		18
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	2	0

Variants in RNF144B

This is a list of pathogenic ClinVar variants found in the RNF144B region.

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

Position	Type	Phenotype	Significance	ClinVar
6-18399560-A-G		not specified	Likely benign (Oct 14, 2023)
6-18399578-A-G		not specified	Uncertain significance (Oct 18, 2021)
6-18399583-C-T		not specified	Uncertain significance (Oct 20, 2021)
6-18399605-C-T		not specified	Likely benign (Dec 19, 2022)
6-18399626-A-C		not specified	Uncertain significance (Oct 26, 2022)
6-18399658-A-G		not specified	Uncertain significance (Jan 09, 2024)
6-18399682-T-G		not specified	Uncertain significance (Sep 08, 2024)
6-18399683-G-A		not specified	Uncertain significance (May 08, 2023)
6-18427623-G-C		not specified	Uncertain significance (Jun 02, 2023)
6-18427636-C-T		not specified	Uncertain significance (Apr 13, 2022)
6-18457163-C-G		not specified	Uncertain significance (May 05, 2023)
6-18457170-C-A		not specified	Uncertain significance (Jul 30, 2024)
6-18457173-A-G		not specified	Uncertain significance (Nov 07, 2022)
6-18457176-G-A		not specified	Uncertain significance (May 18, 2023)
6-18457313-G-A		not specified	Uncertain significance (May 01, 2024)
6-18457316-T-C		not specified	Uncertain significance (Feb 15, 2023)
6-18459615-T-C		not specified	Uncertain significance (Jul 14, 2024)
6-18459632-G-A		not specified	Uncertain significance (Jun 17, 2024)
6-18459660-G-A		not specified	Uncertain significance (Nov 15, 2024)
6-18459674-C-T		not specified	Uncertain significance (Jun 28, 2022)
6-18459708-A-C		not specified	Uncertain significance (Nov 26, 2024)
6-18459717-A-G		not specified	Uncertain significance (Aug 11, 2024)
6-18459720-C-T		not specified	Uncertain significance (Dec 01, 2022)
6-18463334-A-G		not specified	Uncertain significance (May 27, 2022)
6-18463355-C-A		not specified	Uncertain significance (May 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF144B	protein_coding	protein_coding	ENST00000259939	7	100327

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.35e-10	0.241	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.531	151	171	0.886	0.00000877	1975
Missense in Polyphen		43	52.611	0.81731		622
Synonymous	-0.270	67	64.2	1.04	0.00000340	585
Loss of Function	0.692	16	19.3	0.830	0.00000116	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000326	0.000326
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.000272	0.000272
South Asian	0.0000653	0.0000653
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 LCMT2, thereby promoting their degradation. Induces apoptosis via a p53/TP53-dependent but caspase-independent mechanism. However, its overexpression also produces a decrease of the ubiquitin-dependent stability of BAX, a pro-apoptotic protein, ultimately leading to protection of cell death; But, it is not an anti-apoptotic protein per se. {ECO:0000269|PubMed:12853982, ECO:0000269|PubMed:20300062}.
• Pathway: Gastric Cancer Network 2;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Direct p53 effectors (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.644
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• pHI: 0.242
• hipred: Y
• hipred_score: 0.540
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.879

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf144b
• Phenotype: 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hearing/vestibular/ear phenotype; vision/eye phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: protein polyubiquitination;ubiquitin-dependent protein catabolic process;apoptotic process;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;negative regulation of apoptotic process
• Cellular component: ubiquitin ligase complex;cytoplasm;cytosol;integral component of membrane;mitochondrial membrane
• Molecular function: ubiquitin-protein transferase activity;protein binding;ubiquitin conjugating enzyme binding;metal ion binding;ubiquitin protein ligase activity