COA3

cytochrome c oxidase assembly factor 3, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 17:42795147-42798704

Previous symbols: [ "CCDC56" ]

Links

ENSG00000183978 ∙ NCBI:28958 ∙ OMIM:614775 ∙ HGNC:24990 ∙ Uniprot:Q9Y2R0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cytochrome-c oxidase deficiency disease (Supportive), mode of inheritance: AR
• mitochondrial complex IV deficiency, nuclear type 14 (Limited), mode of inheritance: Unknown
• mitochondrial disease (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mitochondrial complex IV deficiency, nuclear type 14	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; Craniofacial; Musculoskeletal; Neurologic	25604084

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COA3 gene.

• not_specified (19 variants)
• not_provided (18 variants)
• Mitochondrial_complex_IV_deficiency,_nuclear_type_1 (2 variants)
• Mitochondrial_complex_IV_deficiency,_nuclear_type_14 (2 variants)
• COA3-related_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COA3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001040431.3. 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				5		5
missense			24	1		25
nonsense						0
start loss						0
frameshift			3			3
splice donor/acceptor (+/-2bp)						0
Total	0	0	27	6	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COA3	protein_coding	protein_coding	ENST00000328434	2	3558

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0648	0.743	125733	0	7	125740	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.189	71	66.7	1.07	0.00000327	649
Missense in Polyphen		22	26.647	0.82562		275
Synonymous	1.47	20	30.3	0.660	0.00000154	252
Loss of Function	0.873	2	3.85	0.520	1.63e-7	40

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Core component of the MITRAC (mitochondrial translation regulation assembly intermediate of cytochrome c oxidase complex) complex, that regulates cytochrome c oxidase assembly. MITRAC complexes regulate both translation of mitochondrial encoded components and assembly of nuclear-encoded components imported in mitochondrion. Required for efficient translation of MT-CO1 and mitochondrial respiratory chain complex IV assembly. {ECO:0000269|PubMed:23260140}.
• Pathway: Thermogenesis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.0929

Intolerance Scores

• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.368
• hipred: N
• hipred_score: 0.250
• ghis: 0.583

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: K

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Coa3

Gene ontology

• Biological process: mitochondrial respiratory chain complex IV assembly;positive regulation of mitochondrial translation
• Cellular component: mitochondrion;integral component of mitochondrial inner membrane
• Molecular function: protein binding