OMA1

OMA1 zinc metallopeptidase, the group of M48 metallopeptidase family

Basic information

Region (hg38): 1:58415384-58546802

Links

ENSG00000162600

∙ NCBI:115209 ∙ OMIM:617081 ∙ HGNC:29661 ∙ Uniprot:Q96E52 ∙ 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 OMA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OMA1 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					2 clinvar	2
missense				4 clinvar	4 clinvar	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1 clinvar	1
Total	0	0	0	4	7

Variants in OMA1

This is a list of pathogenic ClinVar variants found in the OMA1 region.

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

Position	Significance	ClinVar
1-58480975-G-A	Likely benign (Jul 31, 2018)	722109
1-58481183-A-C	Benign (Jun 22, 2018)	780003
1-58506076-T-A	Likely benign (Jan 01, 2023)	2638845
1-58530648-C-A	Likely benign (Jul 19, 2018)	713749
1-58534040-G-A	Benign (May 30, 2018)	785790
1-58534181-T-C	Benign (Jan 23, 2018)	773636
1-58534306-A-G	Likely benign (Dec 20, 2017)	729080
1-58536610-A-C	Benign (Jul 15, 2020)	1287065
1-58536647-A-G	Benign (Jun 10, 2018)	780241
1-58539090-G-A	Benign (Aug 18, 2018)	767673
1-58539094-G-T	Benign (Jun 10, 2018)	780242

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OMA1	protein_coding	protein_coding	ENST00000371226	8	131419

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.22e-11	0.312	125697	0	46	125743	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.494	248	271	0.916	0.0000130	3466
Missense in Polyphen		55	69.703	0.78906		903
Synonymous	0.715	89	98.0	0.908	0.00000486	974
Loss of Function	1.04	20	25.7	0.779	0.00000145	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000415	0.000415
Ashkenazi Jewish	0.00	0.00
East Asian	0.000220	0.000217
Finnish	0.000233	0.000231
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000220	0.000217
South Asian	0.000302	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Metalloprotease that is part of the quality control system in the inner membrane of mitochondria. Following stress conditions that induce loss of mitochondrial membrane potential, mediates cleavage of OPA1 at S1 position, leading to OPA1 inactivation and negative regulation of mitochondrial fusion. May also cleave UQCC3 under these conditions. Its role in mitochondrial quality control is essential for regulating lipid metabolism as well as to maintain body temperature and energy expenditure under cold-stress conditions. {ECO:0000250|UniProtKB:Q9D8H7, ECO:0000269|PubMed:20038677}.;
Pathway: Regulation of Apoptosis;Apoptosis;Programmed Cell Death (Consensus)

Recessive Scores

pRec: 0.0909

Intolerance Scores

loftool: 0.915
rvis_EVS: 1.24
rvis_percentile_EVS: 93.42

Haploinsufficiency Scores

pHI: 0.105
hipred: N
hipred_score: 0.146
ghis: 0.411

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.324

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Oma1
Phenotype: immune system phenotype; liver/biliary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype;

Zebrafish Information Network

Gene name: oma1
Affected structure: head
Phenotype tag: abnormal
Phenotype quality: decreased size

Gene ontology

Biological process: diet induced thermogenesis;glucose metabolic process;protein quality control for misfolded or incompletely synthesized proteins;lipid metabolic process;negative regulation of mitochondrial fusion;mitochondrial protein processing;cristae formation;regulation of apoptotic process;energy homeostasis;positive regulation of cold-induced thermogenesis
Cellular component: mitochondrial inner membrane;integral component of membrane;mitochondrial membrane
Molecular function: metalloendopeptidase activity;metal ion binding