RNF103

ring finger protein 103, the group of Ring finger proteins

Basic information

Region (hg38): 2:86603397-86623866

Previous symbols: [ "ZFP103" ]

Links

ENSG00000239305 ∙ NCBI:7844 ∙ OMIM:602507 ∙ HGNC:12859 ∙ Uniprot:O00237 ∙ 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 RNF103 gene.

• Inborn genetic diseases (27 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF103 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			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in RNF103

This is a list of pathogenic ClinVar variants found in the RNF103 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-86603934-C-T		not specified	Uncertain significance (Jan 26, 2023)
2-86604086-T-G		not specified	Uncertain significance (Sep 27, 2021)
2-86604087-T-C		not specified	Uncertain significance (May 24, 2023)
2-86604177-G-A		not specified	Uncertain significance (Aug 15, 2023)
2-86604285-G-C		not specified	Uncertain significance (Mar 16, 2022)
2-86604312-T-G		not specified	Uncertain significance (Oct 26, 2021)
2-86604317-C-T		not specified	Uncertain significance (Dec 09, 2023)
2-86604354-C-T		not specified	Uncertain significance (Dec 07, 2021)
2-86604421-C-T		not specified	Uncertain significance (Mar 16, 2022)
2-86604558-T-C		not specified	Uncertain significance (Aug 02, 2021)
2-86604582-C-T		not specified	Uncertain significance (Nov 10, 2022)
2-86604595-T-C		not specified	Uncertain significance (Dec 06, 2022)
2-86605082-G-C		not specified	Uncertain significance (Jun 21, 2021)
2-86605091-A-T		not specified	Uncertain significance (Jun 22, 2023)
2-86605140-C-G		not specified	Uncertain significance (Sep 27, 2021)
2-86605189-A-G		not specified	Uncertain significance (Oct 14, 2023)
2-86605209-T-C		not specified	Uncertain significance (Mar 16, 2022)
2-86605217-A-T		not specified	Uncertain significance (Jul 06, 2021)
2-86605317-C-T		not specified	Uncertain significance (Jun 12, 2023)
2-86605323-C-T		not specified	Uncertain significance (Aug 14, 2023)
2-86605353-G-A		not specified	Uncertain significance (Nov 21, 2022)
2-86605380-A-G		not specified	Uncertain significance (Jun 22, 2021)
2-86612177-T-C		not specified	Uncertain significance (Jan 23, 2024)
2-86612225-T-C		not specified	Uncertain significance (Jun 06, 2023)
2-86612244-C-G		not specified	Uncertain significance (Aug 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNF103	protein_coding	protein_coding	ENST00000237455	4	20474

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.897	0.103	125738	0	10	125748	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.836	315	360	0.876	0.0000177	4521
Missense in Polyphen		109	148.57	0.73365		1873
Synonymous	-0.706	143	133	1.08	0.00000656	1260
Loss of Function	4.17	5	29.4	0.170	0.00000159	354

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as an E2-dependent E3 ubiquitin-protein ligase, probably involved in the ER-associated protein degradation pathway. {ECO:0000269|PubMed:10500182, ECO:0000269|PubMed:18675248}.
• Pathway: ER Quality Control Compartment (ERQC);Calnexin/calreticulin cycle;Post-translational protein modification;Metabolism of proteins;Asparagine N-linked glycosylation;N-glycan trimming in the ER and Calnexin/Calreticulin cycle (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.249
• rvis_EVS: -0.15
• rvis_percentile_EVS: 42.23

Haploinsufficiency Scores

• pHI: 0.915
• hipred: Y
• hipred_score: 0.595
• ghis: 0.540

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.882

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf103
• Phenotype: 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: central nervous system development;protein ubiquitination;ubiquitin-dependent ERAD pathway;endoplasmic reticulum mannose trimming
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;endoplasmic reticulum quality control compartment
• Molecular function: ubiquitin-protein transferase activity;protein binding;metal ion binding;ubiquitin protein ligase activity