COA1

cytochrome c oxidase assembly factor 1, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 7:43608455-43729717

Previous symbols: [ "C7orf44" ]

Links

ENSG00000106603 ∙ NCBI:55744 ∙ OMIM:614769 ∙ HGNC:21868 ∙ Uniprot:Q9GZY4 ∙ 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 COA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COA1 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						0
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in COA1

This is a list of pathogenic ClinVar variants found in the COA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-43619643-A-T		not specified	Uncertain significance (Mar 06, 2023)
7-43619645-A-C		not specified	Uncertain significance (Sep 22, 2023)
7-43623585-T-C			Benign (Sep 11, 2018)
7-43623617-T-C		not specified	Uncertain significance (Nov 30, 2022)
7-43623729-A-G		not specified	Uncertain significance (Apr 06, 2023)
7-43623765-A-G		not specified	Uncertain significance (Feb 14, 2023)
7-43623766-T-A		not specified	Uncertain significance (Aug 11, 2022)
7-43623782-T-C		not specified	Uncertain significance (Jan 26, 2023)
7-43624552-C-T		not specified	Uncertain significance (May 23, 2023)
7-43624733-G-C		not specified	Uncertain significance (Aug 02, 2021)
7-43624799-A-C		not specified	Uncertain significance (Mar 01, 2024)
7-43639604-C-T		not specified	Uncertain significance (Jun 23, 2021)
7-43639609-T-G		not specified	Uncertain significance (Dec 28, 2023)
7-43640585-C-T		not specified	Uncertain significance (Aug 13, 2021)
7-43640604-C-T		not specified	Uncertain significance (Nov 08, 2021)
7-43645313-G-A		not specified	Uncertain significance (Oct 29, 2021)
7-43645337-C-T		not specified	Uncertain significance (Jan 17, 2024)
7-43647552-A-T		not specified	Uncertain significance (Mar 02, 2023)
7-43647568-C-T		not specified	Uncertain significance (Aug 21, 2023)
7-43647634-A-T		not specified	Uncertain significance (Feb 28, 2024)
7-43648608-A-G		not specified	Uncertain significance (Aug 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COA1	protein_coding	protein_coding	ENST00000395879	5	121262

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00883	0.817	125731	1	16	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.440	70	81.2	0.862	0.00000411	955
Missense in Polyphen		22	26.147	0.84138		317
Synonymous	0.128	32	32.9	0.972	0.00000206	271
Loss of Function	1.07	4	7.08	0.565	2.98e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.000163	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: 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 assembly of mitochondrial respiratory chain complex I and complex IV. {ECO:0000269|PubMed:23260140}.
• Pathway: Thermogenesis - Homo sapiens (human) (Consensus)

Intolerance Scores

• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.0384
• hipred: N
• hipred_score: 0.123
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Gene ontology

• Biological process: mitochondrial respiratory chain complex I assembly;mitochondrial respiratory chain complex IV assembly
• Cellular component: mitochondrion;cytosol;integral component of mitochondrial inner membrane