TACO1

translational activator of cytochrome c oxidase I, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 17:63600882-63608365

Previous symbols: [ "CCDC44" ]

Links

ENSG00000136463 ∙ NCBI:51204 ∙ OMIM:612958 ∙ HGNC:24316 ∙ Uniprot:Q9BSH4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• mitochondrial complex IV deficiency, nuclear type 8 (Strong), mode of inheritance: AR
• Leigh syndrome with leukodystrophy (Supportive), mode of inheritance: AR
• mitochondrial complex IV deficiency, nuclear type 8 (Moderate), mode of inheritance: AR
• mitochondrial complex IV deficiency, nuclear type 8 (Strong), mode of inheritance: AR
• Leigh syndrome (Moderate), mode of inheritance: AR
• mitochondrial disease (Definitive), mode of inheritance: AR
• mitochondrial complex IV deficiency, nuclear type 8 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mitochondrial complex IV deficiency, nuclear type 8	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	Biochemical; Musculoskeletal; Neurologic	19503089

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TACO1 gene.

• not_provided (95 variants)
• Mitochondrial_complex_IV_deficiency,_nuclear_type_8 (51 variants)
• Inborn_genetic_diseases (36 variants)
• Mitochondrial_complex_IV_deficiency,_nuclear_type_1 (17 variants)
• not_specified (8 variants)
• TACO1-related_disorder (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TACO1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016360.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			3	31		34
missense		2	81	8	1	92
nonsense	1	3				4
start loss						0
frameshift	1	7	1			9
splice donor/acceptor (+/-2bp)		3				3
Total	2	15	85	39	1

Highest pathogenic variant AF is 0.00003965633

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TACO1	protein_coding	protein_coding	ENST00000258975	5	7495

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.938	133	167	0.796	0.00000868	1927
Missense in Polyphen		34	46.98	0.72371		601
Synonymous	-0.570	76	69.9	1.09	0.00000385	612
Loss of Function	1.37	6	10.9	0.552	5.46e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000243	0.000243
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000884	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000982	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a translational activator of mitochondrially- encoded cytochrome c oxidase 1. {ECO:0000269|PubMed:19503089}.
• Disease: DISEASE: Leigh syndrome (LS) [MIM:256000]: An early-onset progressive neurodegenerative disorder characterized by the presence of focal, bilateral lesions in one or more areas of the central nervous system including the brainstem, thalamus, basal ganglia, cerebellum and spinal cord. Clinical features depend on which areas of the central nervous system are involved and include subacute onset of psychomotor retardation, hypotonia, ataxia, weakness, vision loss, eye movement abnormalities, seizures, and dysphagia. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Respiratory electron transport;The citric acid (TCA) cycle and respiratory electron transport;Metabolism;TP53 Regulates Metabolic Genes;Transcriptional Regulation by TP53;Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. (Consensus)

Recessive Scores

• pRec: 0.240

Intolerance Scores

• loftool: 0.565
• rvis_EVS: -0.18
• rvis_percentile_EVS: 39.95

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of translation
• Cellular component: nucleus;mitochondrion
• Molecular function: protein binding