RNF123

ring finger protein 123, the group of Armadillo like helical domain containing|Ring finger proteins

Basic information

Region (hg38): 3:49689538-49721529

Links

ENSG00000164068 ∙ NCBI:63891 ∙ OMIM:614472 ∙ HGNC:21148 ∙ Uniprot:Q5XPI4 ∙ 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 RNF123 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF123 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			91	1	1	93
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			31	1	1	33
Total	0	0	122	3	3

Variants in RNF123

This is a list of pathogenic ClinVar variants found in the RNF123 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-49691169-G-T		not specified	Uncertain significance (May 08, 2024)
3-49691175-A-G		not specified	Uncertain significance (May 14, 2024)
3-49691181-G-A		not specified	Uncertain significance (Mar 04, 2024)
3-49691199-C-T		not specified	Uncertain significance (Jan 03, 2024)
3-49691200-G-C		not specified	Uncertain significance (Jul 14, 2023)
3-49691205-A-T		not specified	Uncertain significance (Oct 26, 2022)
3-49691233-A-G		not specified	Uncertain significance (Jul 17, 2023)
3-49697147-C-T		not specified	Uncertain significance (May 13, 2024)
3-49697210-G-A		not specified	Uncertain significance (Jul 05, 2022)
3-49698124-G-A		not specified	Uncertain significance (Dec 28, 2023)
3-49698776-G-A		not specified	Uncertain significance (Dec 17, 2021)
3-49699075-T-C		not specified	Uncertain significance (May 30, 2023)
3-49699096-G-A		not specified	Uncertain significance (May 24, 2023)
3-49699487-C-T		not specified	Uncertain significance (Nov 06, 2023)
3-49699523-C-T		not specified	Uncertain significance (Apr 08, 2024)
3-49699526-G-A		not specified	Uncertain significance (Sep 16, 2021)
3-49699675-G-A		not specified	Uncertain significance (Mar 04, 2024)
3-49699681-T-C		not specified	Uncertain significance (Sep 17, 2021)
3-49700258-T-C		not specified	Uncertain significance (Apr 04, 2023)
3-49700278-G-A		not specified	Uncertain significance (Dec 02, 2021)
3-49700311-G-A		not specified	Uncertain significance (Jan 24, 2024)
3-49700506-T-C		not specified	Uncertain significance (Jun 04, 2024)
3-49700649-G-C		not specified	Uncertain significance (Oct 27, 2021)
3-49700657-A-G		not specified	Uncertain significance (Apr 22, 2024)
3-49700684-C-T		not specified	Uncertain significance (Apr 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF123	protein_coding	protein_coding	ENST00000327697	38	32031

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000847	1.00	125693	0	55	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.65	672	804	0.836	0.0000521	8466
Missense in Polyphen		196	276.82	0.70805		2914
Synonymous	0.360	318	326	0.975	0.0000199	2669
Loss of Function	5.57	22	73.5	0.299	0.00000342	826

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000698	0.000688
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000217	0.000217
Finnish	0.000186	0.000185
European (Non-Finnish)	0.000222	0.000220
Middle Eastern	0.000217	0.000217
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalytic subunit of the KPC complex that acts as E3 ubiquitin-protein ligase. Required for poly-ubiquitination and proteasome-mediated degradation of CDKN1B during G1 phase of the cell cycle. {ECO:0000269|PubMed:15531880, ECO:0000269|PubMed:16227581}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Ub-specific processing proteases;Deubiquitination (Consensus)

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.604
• rvis_EVS: -1.12
• rvis_percentile_EVS: 6.61

Haploinsufficiency Scores

• pHI: 0.227
• hipred: Y
• hipred_score: 0.648
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.518

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf123

Gene ontology

• Biological process: protein ubiquitination;protein deubiquitination;proteolysis involved in cellular protein catabolic process
• Cellular component: cytoplasm;cytosol;nuclear membrane
• Molecular function: ubiquitin-protein transferase activity;metal ion binding