TACO1

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

Basic information

Region (hg38): 17:63600881-63608365

Previous symbols: [ "CCDC44" ]

Links

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

Phenotypes

GenCC

Source: genCC

• cytochrome-c oxidase deficiency disease (Strong), mode of inheritance: AR
• mitochondrial complex 4 deficiency, nuclear type 8 (Strong), mode of inheritance: AR
• Leigh syndrome with leukodystrophy (Supportive), mode of inheritance: AR
• mitochondrial complex 4 deficiency, nuclear type 8 (Moderate), mode of inheritance: AR
• Leigh syndrome (Moderate), 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.

• Mitochondrial complex 4 deficiency, nuclear type 8 (1 variants)
• Mitochondrial complex IV deficiency, nuclear type 1 (1 variants)
• not provided (1 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.

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	22		24
missense		1	45	3	1	50
nonsense	1					1
start loss						0
frameshift	1	5				6
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region			1			1
non coding			8	9	9	26
Total	2	7	55	34	10

Highest pathogenic variant AF is 0.0000131

Variants in TACO1

This is a list of pathogenic ClinVar variants found in the TACO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-63600907-C-T		Mitochondrial complex IV deficiency, nuclear type 1	Uncertain significance (Jan 12, 2018)
17-63600916-A-G		Mitochondrial complex IV deficiency, nuclear type 1	Uncertain significance (Jan 12, 2018)
17-63600921-A-G		Mitochondrial complex IV deficiency, nuclear type 1	Uncertain significance (Jan 12, 2018)
17-63601100-C-T		Inborn genetic diseases	Uncertain significance (Sep 20, 2023)
17-63601110-A-G		Mitochondrial complex 4 deficiency, nuclear type 8	Likely benign (Aug 16, 2021)
17-63601125-C-G			Likely benign (Jun 01, 2022)
17-63601136-T-C		Inborn genetic diseases	Uncertain significance (Jun 18, 2021)
17-63601149-C-T		Mitochondrial complex 4 deficiency, nuclear type 8	Likely benign (Feb 24, 2022)
17-63601150-G-A			Uncertain significance (Dec 03, 2021)
17-63601156-A-G		Inborn genetic diseases	Conflicting classifications of pathogenicity (Apr 24, 2024)
17-63601158-G-C			Uncertain significance (Jan 28, 2022)
17-63601159-G-C		Inborn genetic diseases	Uncertain significance (Jun 11, 2024)
17-63601174-G-A		Inborn genetic diseases	Uncertain significance (Feb 12, 2024)
17-63601175-AC-A			Likely pathogenic (Sep 15, 2022)
17-63601175-A-AC		Mitochondrial complex IV deficiency, nuclear type 1	Pathogenic (Apr 17, 2018)
17-63601181-G-A			Uncertain significance (Sep 15, 2014)
17-63601182-G-A			Likely benign (Jul 17, 2022)
17-63601190-A-C		Inborn genetic diseases	Uncertain significance (Apr 01, 2021)
17-63601210-G-A			Uncertain significance (Jul 07, 2023)
17-63601215-C-A		TACO1-related disorder	Likely benign (Feb 09, 2022)
17-63601239-T-C			Likely benign (Aug 09, 2022)
17-63601258-G-A			Uncertain significance (May 21, 2022)
17-63601263-C-A			Uncertain significance (Nov 06, 2023)
17-63601287-C-T			Likely benign (Jun 13, 2018)
17-63601289-T-A		Inborn genetic diseases	Uncertain significance (Mar 29, 2022)

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
0.00146	0.884	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

Haploinsufficiency Scores

• pHI: 0.0664
• hipred: N
• hipred_score: 0.278
• ghis: 0.533

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

Mouse Genome Informatics

• Gene name: Taco1
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; vision/eye phenotype; 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); pigmentation phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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)

Gene ontology

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