OXA1L

OXA1L mitochondrial inner membrane protein, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 14:22766522-22773042

Links

ENSG00000155463 ∙ NCBI:5018 ∙ OMIM:601066 ∙ HGNC:8526 ∙ Uniprot:Q15070 ∙ 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 OXA1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OXA1L 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	2
missense			36	6	2	44
nonsense						0
start loss						0
frameshift				1		1
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				1		1
Total	0	0	36	9	4

Variants in OXA1L

This is a list of pathogenic ClinVar variants found in the OXA1L region.

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

Position	Type	Phenotype	Significance	ClinVar
14-22766593-T-C		OXA1L-related disorder	Likely benign (Dec 11, 2023)
14-22766599-G-A			Benign (Mar 03, 2015)
14-22766611-C-G		not specified	Likely benign (Sep 17, 2021)
14-22766613-G-C			Likely benign (Mar 01, 2022)
14-22766676-C-CA			Likely benign (Mar 01, 2022)
14-22766682-C-T		not specified	Likely benign (May 17, 2023)
14-22766688-C-T		not specified	Uncertain significance (Oct 27, 2021)
14-22766694-C-G		not specified	Uncertain significance (Mar 23, 2023)
14-22766696-G-A		not specified	Uncertain significance (Jan 31, 2023)
14-22766708-A-G		not specified	Uncertain significance (Mar 07, 2023)
14-22766718-T-C		not specified	Uncertain significance (Jan 30, 2024)
14-22766722-C-G		not specified	Uncertain significance (Jul 20, 2021)
14-22766727-G-C		not specified	Uncertain significance (Oct 12, 2022)
14-22766746-G-C		not specified	Uncertain significance (Aug 12, 2022)
14-22766759-C-A		not specified	Uncertain significance (Dec 07, 2023)
14-22766759-C-G		not specified	Uncertain significance (May 30, 2023)
14-22766760-G-C		not specified	Uncertain significance (Dec 14, 2023)
14-22767257-G-A		not specified	Uncertain significance (Aug 13, 2021)
14-22767279-T-C		not specified	Likely benign (Aug 12, 2021)
14-22767302-C-T		not specified	Uncertain significance (Jan 16, 2024)
14-22767321-C-G		not specified	Likely benign (Jan 03, 2022)
14-22767345-T-C		not specified	Uncertain significance (May 02, 2024)
14-22767348-T-C		not specified	Uncertain significance (Nov 21, 2023)
14-22767417-G-C		OXA1L-related disorder	Likely benign (Aug 16, 2023)
14-22767977-T-C		not specified	Uncertain significance (Apr 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OXA1L	protein_coding	protein_coding	ENST00000285848	10	5277

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.87e-10	0.628	125683	0	64	125747	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.956	332	286	1.16	0.0000152	3179
Missense in Polyphen		61	54.426	1.1208		569
Synonymous	-2.49	137	105	1.31	0.00000530	1034
Loss of Function	1.38	19	26.7	0.712	0.00000148	267

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000571	0.000572
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.000416	0.000416
European (Non-Finnish)	0.000246	0.000246
Middle Eastern	0.000326	0.000326
South Asian	0.000163	0.000163
Other	0.000489	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the insertion of integral membrane proteins into the mitochondrial inner membrane. Essential for the activity and assembly of cytochrome oxidase. Required for the correct biogenesis of ATP synthase and complex I in mitochondria. {ECO:0000269|PubMed:17936786, ECO:0000269|PubMed:7991568}.
• Pathway: Protein export - Homo sapiens (human);Mitochondrial translation initiation;Translation;Metabolism of proteins;Mitochondrial translation elongation;Mitochondrial translation termination;Mitochondrial translation (Consensus)

Recessive Scores

• pRec: 0.0905

Intolerance Scores

• loftool: 0.903
• rvis_EVS: 0.94
• rvis_percentile_EVS: 89.86

Haploinsufficiency Scores

• pHI: 0.0742
• hipred: N
• hipred_score: 0.123
• ghis: 0.425

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.827

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Oxa1l

Gene ontology

• Biological process: aerobic respiration;protein transport;negative regulation of ATPase activity;protein insertion into mitochondrial inner membrane from matrix;mitochondrial respiratory chain complex I assembly;mitochondrial proton-transporting ATP synthase complex assembly;mitochondrial respiratory chain complex IV assembly;protein insertion into membrane;protein tetramerization;negative regulation of oxidoreductase activity;oxidation-reduction process;protein-containing complex assembly;mitochondrial translational elongation;mitochondrial translational termination
• Cellular component: mitochondrion;mitochondrial respirasome;mitochondrial matrix;integral component of mitochondrial inner membrane;mitochondrial membrane;integral component of mitochondrial membrane;protein-containing complex
• Molecular function: protein binding;membrane insertase activity;protein homodimerization activity;mitochondrial ribosome binding