OBI1

ORC ubiquitin ligase 1, the group of Ring finger proteins

Basic information

Region (hg38): 13:78614288-78659155

Previous symbols: [ "C13orf7", "RNF219" ]

Links

ENSG00000152193 ∙ NCBI:79596 ∙ OMIM:615906 ∙ HGNC:20308 ∙ Uniprot:Q5W0B1 ∙ 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 OBI1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OBI1 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			42			42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	0	0

Variants in OBI1

This is a list of pathogenic ClinVar variants found in the OBI1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-78615621-T-C		not specified	Uncertain significance (Jan 18, 2022)
13-78615623-C-T		not specified	Uncertain significance (Jan 23, 2024)
13-78615662-T-C		not specified	Uncertain significance (Jun 13, 2024)
13-78615677-A-C		not specified	Uncertain significance (Jun 07, 2023)
13-78615713-T-C		not specified	Uncertain significance (Jul 19, 2023)
13-78615722-T-C		not specified	Uncertain significance (Jun 29, 2022)
13-78615723-G-A		not specified	Uncertain significance (Mar 02, 2023)
13-78615769-T-G		not specified	Uncertain significance (Feb 16, 2023)
13-78615782-T-C		not specified	Uncertain significance (Apr 18, 2023)
13-78615914-G-A		not specified	Uncertain significance (Jan 26, 2022)
13-78616034-A-G		not specified	Uncertain significance (Jul 20, 2021)
13-78616079-G-A		not specified	Uncertain significance (Feb 28, 2024)
13-78616106-T-C		not specified	Uncertain significance (Jun 07, 2024)
13-78616223-G-C		not specified	Uncertain significance (May 17, 2023)
13-78616230-A-T		not specified	Uncertain significance (Nov 18, 2023)
13-78616340-T-C		not specified	Uncertain significance (Apr 25, 2022)
13-78616422-T-C		not specified	Uncertain significance (Apr 25, 2022)
13-78616441-T-G		not specified	Uncertain significance (Jun 13, 2024)
13-78616482-C-A		not specified	Uncertain significance (Apr 07, 2022)
13-78616511-T-C		not specified	Uncertain significance (Dec 13, 2023)
13-78616602-G-A		not specified	Uncertain significance (May 01, 2024)
13-78616618-T-A		not specified	Uncertain significance (Feb 28, 2024)
13-78616728-A-G		not specified	Uncertain significance (Aug 10, 2023)
13-78616793-G-A		not specified	Uncertain significance (May 21, 2024)
13-78616799-C-T		not specified	Uncertain significance (Sep 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OBI1	protein_coding	protein_coding	ENST00000282003	6	44889

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.86e-8	0.973	125666	1	81	125748	0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.151	374	366	1.02	0.0000175	4827
Missense in Polyphen		122	120.98	1.0084		1557
Synonymous	-0.285	137	133	1.03	0.00000624	1325
Loss of Function	2.11	16	28.1	0.570	0.00000144	392

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00118	0.00112
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000379	0.000369
Middle Eastern	0.000163	0.000163
South Asian	0.000263	0.000261
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0932

Intolerance Scores

• loftool: 0.374
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.36

Haploinsufficiency Scores

• pHI: 0.706
• hipred: N
• hipred_score: 0.254
• ghis: 0.613

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.670

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rnf219

Gene ontology

• Molecular function: protein binding;metal ion binding