RNF144A

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

Basic information

Region (hg38): 2:6917411-7068286

Previous symbols: [ "RNF144" ]

Links

ENSG00000151692 ∙ NCBI:9781 ∙ OMIM:619454 ∙ HGNC:20457 ∙ Uniprot:P50876 ∙ 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 RNF144A gene.

• Inborn genetic diseases (16 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF144A 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	2
missense			14	2		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	3	1

Variants in RNF144A

This is a list of pathogenic ClinVar variants found in the RNF144A region.

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

Position	Type	Phenotype	Significance	ClinVar
2-6997026-A-G		not specified	Uncertain significance (Jul 06, 2021)
2-7014502-G-A		not specified	Uncertain significance (Aug 08, 2023)
2-7014502-G-T		not specified	Uncertain significance (Mar 07, 2024)
2-7014742-C-G		not specified	Uncertain significance (Dec 19, 2022)
2-7014762-A-C		not specified	Uncertain significance (Nov 21, 2023)
2-7020544-G-A		not specified	Likely benign (Oct 14, 2021)
2-7020573-G-C		not specified	Uncertain significance (Jul 05, 2023)
2-7020587-G-A		not specified	Likely benign (Dec 13, 2021)
2-7020645-G-C		not specified	Uncertain significance (Apr 20, 2023)
2-7020656-T-G		not specified	Uncertain significance (Dec 28, 2022)
2-7024394-G-A		not specified	Uncertain significance (Dec 03, 2021)
2-7024397-G-A		not specified	Uncertain significance (Oct 13, 2023)
2-7024420-G-C		not specified	Uncertain significance (Dec 01, 2022)
2-7024433-A-G		not specified	Uncertain significance (May 09, 2023)
2-7024447-A-G			Benign (Jan 30, 2020)
2-7024453-C-T			Likely benign (Feb 01, 2023)
2-7030152-T-A		not specified	Uncertain significance (Mar 01, 2024)
2-7030178-G-A		not specified	Uncertain significance (Dec 15, 2022)
2-7039638-A-G		not specified	Uncertain significance (Jun 24, 2022)
2-7039692-G-A		not specified	Uncertain significance (Sep 16, 2021)
2-7039695-A-G		not specified	Uncertain significance (Aug 17, 2022)
2-7039747-C-T		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF144A	protein_coding	protein_coding	ENST00000320892	7	150895

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.948	0.0522	125732	0	2	125734	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.44	124	178	0.697	0.0000105	1916
Missense in Polyphen		45	79.108	0.56884		849
Synonymous	-0.614	80	73.3	1.09	0.00000494	550
Loss of Function	3.51	2	18.1	0.110	9.58e-7	183

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000881	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
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. Mediates the ubiquitination and degradation of the DNA damage kinase PRKDC. {ECO:0000250, ECO:0000269|PubMed:24979766}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Protein ubiquitination;E3 ubiquitin ligases ubiquitinate target proteins (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.152
• hipred: Y
• hipred_score: 0.654
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.790

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf144a

Gene ontology

• Biological process: protein polyubiquitination;ubiquitin-dependent protein catabolic process;protein ubiquitination;positive regulation of proteasomal ubiquitin-dependent protein catabolic process
• Cellular component: ubiquitin ligase complex;cytoplasm;Golgi apparatus;plasma membrane;endosome membrane;integral component of membrane;cytoplasmic vesicle membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding;ubiquitin conjugating enzyme binding;metal ion binding;ubiquitin protein ligase activity