OBI1

protein-coding

ORC ubiquitin ligase 1, the group of Ring finger proteins

Gene summary

Enables chromatin binding activity and ubiquitin-protein transferase activity. Involved in protein autoubiquitination; protein monoubiquitination; and regulation of DNA replication. Located in chromatin. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C13orf7
RNF219

MANE transcript

NM_024546.4

Inheritance

—

ClinVar variants

U:107B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.57

Max pathogenic AF

—

Genomic locus

chr13:78,614,289-78,659,155

External References & Databases

Ensembl (ENSG00000152193)

Transcript & Mutation Effects

hg38 • Region Span ~44.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to OBI1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 107

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024546.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			106 clinvar	3 clinvar		109
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	107	3	0	110

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024546.4	RefSeq	NP_078822.3	6	MANE Select
ENST00000282003.7	Ensembl	ENSP00000282003.6	6	MANE Select
ENST00000880927.1	Ensembl	ENSP00000550986.1	6	Standard
ENST00000880927.2	Ensembl	ENSP00000550986.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
metal ion binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000282003
Coding exons: 6
Length: 44889
Individuals with no LoFs: 125666
Homozygous LoFs: 1
Heterozygous LoFs: 81
Defined: 125748
p: 0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.151	374	366	1.02	0.0000175	4827
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00080	0.00074	rare
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00016	0.00016	rare
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.00038	0.00037	rare
South Asian	0.00026	0.00026	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0932

Intolerance Scores

LoFtool: 0.374
RVIS EVS: -0.11
RVIS percentile EVS: 45.36

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.670

Gene Damage Prediction

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