COX19

cytochrome c oxidase assembly factor COX19, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 7:898778-975549

Links

ENSG00000240230 ∙ NCBI:90639 ∙ OMIM:610429 ∙ HGNC:28074 ∙ Uniprot:Q49B96 ∙ 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 COX19 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COX19 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			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	1	0

Variants in COX19

This is a list of pathogenic ClinVar variants found in the COX19 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-899087-C-T		not specified	Uncertain significance (Sep 18, 2024)
7-899138-C-T		not specified	Uncertain significance (Jun 09, 2022)
7-899208-C-T			Benign (Jun 18, 2018)
7-899233-A-G		not specified	Uncertain significance (Apr 28, 2023)
7-899486-G-C		not specified	Uncertain significance (Aug 05, 2024)
7-900538-C-T		not specified	Uncertain significance (Jul 12, 2022)
7-900597-T-C		not specified	Uncertain significance (Sep 11, 2024)
7-904137-C-G		not specified	Uncertain significance (May 29, 2024)
7-904206-C-T		not specified	Uncertain significance (Sep 17, 2021)
7-904251-T-C		not specified	Uncertain significance (Feb 28, 2023)
7-905070-T-C		not specified	Uncertain significance (May 16, 2022)
7-905112-T-C		not specified	Uncertain significance (Nov 25, 2024)
7-905115-C-T		not specified	Uncertain significance (Aug 10, 2023)
7-905132-G-C		not specified	Uncertain significance (Aug 21, 2024)
7-905146-G-A		not specified	Uncertain significance (Dec 15, 2022)
7-905146-G-C		not specified	Uncertain significance (Apr 22, 2024)
7-905167-G-A		not specified	Uncertain significance (May 31, 2023)
7-905180-G-C			Benign (Jun 18, 2018)
7-919976-T-G		not specified	Uncertain significance (Dec 16, 2023)
7-919979-G-A		not specified	Uncertain significance (Feb 22, 2023)
7-920009-T-C		not specified	Uncertain significance (Nov 13, 2024)
7-920050-C-G		not specified	Uncertain significance (May 30, 2023)
7-926574-C-T		not specified	Uncertain significance (Sep 25, 2023)
7-926616-G-A		not specified	Uncertain significance (Jan 04, 2022)
7-926616-G-T		not specified	Uncertain significance (Aug 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COX19	protein_coding	protein_coding	ENST00000344111	3	76821

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00432	0.446	124971	0	5	124976	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.02	62	43.1	1.44	0.00000185	600
Missense in Polyphen		20	17.24	1.1601		219
Synonymous	-1.04	21	15.7	1.33	7.07e-7	136
Loss of Function	-0.374	3	2.38	1.26	9.96e-8	37

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000386	0.0000353
Middle Eastern	0.00	0.00
South Asian	0.0000343	0.0000330
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for the transduction of an SCO1-dependent redox signal from the mitochondrion to ATP7A to regulate cellular copper homeostasis (PubMed:23345593). May be required for the assembly of mitochondrial cytochrome c oxidase (By similarity). {ECO:0000250|UniProtKB:Q3E731, ECO:0000269|PubMed:23345593}.
• Pathway: Thermogenesis - Homo sapiens (human);Metabolism of proteins;Mitochondrial protein import (Consensus)

Recessive Scores

• pRec: 0.0885

Intolerance Scores

• loftool: 0.593
• rvis_EVS: 0.37
• rvis_percentile_EVS: 74.95

Haploinsufficiency Scores

• pHI: 0.0293
• hipred: N
• hipred_score: 0.340
• ghis: 0.438

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: K
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cox19
• 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: cellular copper ion homeostasis;mitochondrial respiratory chain complex IV assembly
• Cellular component: mitochondrion;mitochondrial intermembrane space;cytosol
• Molecular function: protein binding