OXR1

oxidation resistance 1, the group of TLDc domain containing

Basic information

Region (hg38): 8:106270143-106752694

Links

ENSG00000164830 ∙ NCBI:55074 ∙ OMIM:605609 ∙ HGNC:15822 ∙ Uniprot:Q8N573 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• isolated cerebellar hypoplasia/agenesis (Moderate), mode of inheritance: AR
• isolated cerebellar hypoplasia/agenesis (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cerebellar hypoplasia/atrophy, epilepsy, and global developmental delay	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	31785787

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OXR1 gene.

• Inborn genetic diseases (34 variants)
• not provided (7 variants)
• Congenital cerebellar hypoplasia (5 variants)
• - (2 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OXR1 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
missense			39			39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			3			3
non coding						0
Total	0	0	39	0	1

Variants in OXR1

This is a list of pathogenic ClinVar variants found in the OXR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-106519025-G-A		Inborn genetic diseases	Uncertain significance (May 18, 2023)
8-106519050-C-A		Inborn genetic diseases	Uncertain significance (Jun 19, 2021)
8-106658026-C-T		Congenital cerebellar hypoplasia	Uncertain significance (Sep 02, 2022)
8-106658090-G-A		Inborn genetic diseases	Uncertain significance (Jun 29, 2022)
8-106679204-T-TC		OXR1-related disorder	Likely benign (Jan 15, 2021)
8-106679222-A-G		Hearing impairment	Conflicting classifications of pathogenicity (Mar 17, 2023)
8-106679270-C-G		Inborn genetic diseases	Uncertain significance (Dec 14, 2023)
8-106684327-A-G		Inborn genetic diseases	Uncertain significance (Oct 14, 2023)
8-106684358-C-T		Inborn genetic diseases	Uncertain significance (Feb 07, 2022)
8-106692712-TAAA-T		OXR1-related disorder	Likely benign (Oct 22, 2020)
8-106692741-A-C		Inborn genetic diseases	Uncertain significance (Oct 10, 2023)
8-106692777-G-A		Inborn genetic diseases	Uncertain significance (Jun 10, 2022)
8-106692783-G-A		Inborn genetic diseases	Uncertain significance (Jan 24, 2024)
8-106692797-G-C		Inborn genetic diseases	Uncertain significance (Apr 08, 2022)
8-106692810-C-T		Inborn genetic diseases	Uncertain significance (Nov 03, 2023)
8-106692816-A-C		Inborn genetic diseases	Uncertain significance (Jun 02, 2021)
8-106692827-T-A		Inborn genetic diseases	Uncertain significance (Dec 20, 2022)
8-106702924-C-A		Inborn genetic diseases	Uncertain significance (Feb 28, 2023)
8-106703077-G-A		Inborn genetic diseases	Uncertain significance (Dec 13, 2023)
8-106706387-T-C		Inborn genetic diseases	Uncertain significance (Jun 17, 2022)
8-106706393-A-T		Inborn genetic diseases	Uncertain significance (Apr 28, 2022)
8-106706430-G-T		Inborn genetic diseases	Uncertain significance (Jun 17, 2022)
8-106706452-A-G		Inborn genetic diseases	Uncertain significance (Dec 02, 2022)
8-106706468-G-A		Inborn genetic diseases	Uncertain significance (Jul 20, 2021)
8-106706480-A-G			Uncertain significance (Dec 20, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OXR1	protein_coding	protein_coding	ENST00000442977	16	482450

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.841	0.159	125728	0	12	125740	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.02	380	440	0.864	0.0000213	5749
Missense in Polyphen		101	166.68	0.60596		2221
Synonymous	-0.836	165	152	1.09	0.00000778	1612
Loss of Function	5.03	9	45.7	0.197	0.00000266	547

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000127	0.000127
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000537	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in protection from oxidative damage. {ECO:0000269|PubMed:11114193, ECO:0000269|PubMed:15060142}.

Recessive Scores

• pRec: 0.106

Intolerance Scores

• loftool: 0.668
• rvis_EVS: -1.09
• rvis_percentile_EVS: 7.15

Haploinsufficiency Scores

• pHI: 0.182
• hipred: N
• hipred_score: 0.492
• ghis: 0.637

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.247

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Oxr1
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); cellular phenotype

Gene ontology

• Biological process: response to oxidative stress;adult walking behavior;negative regulation of neuron apoptotic process;neuron apoptotic process;oxidation-reduction process;cellular response to hydroperoxide;negative regulation of peptidyl-cysteine S-nitrosylation;negative regulation of oxidative stress-induced neuron death
• Cellular component: cellular_component;nucleoplasm;nucleolus;mitochondrion;intracellular membrane-bounded organelle
• Molecular function: molecular_function;oxidoreductase activity