COX19

protein-coding

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

Gene summary

COX19 encodes a cytochrome c oxidase (COX)-assembly protein. The S. cerevisiae Cox19 protein may play a role in metal transport to the mitochondrial intermembrane space and assembly of complex IV of the mitochondrial respiratory chain (Sacconi et al., 2005 [PubMed 16212937]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_001031617.3

Inheritance

—

ClinVar variants

U:15B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.26

Max pathogenic AF

—

Genomic locus

chr7:898,778-975,549

External References & Databases

Ensembl (ENSG00000240230)

Transcript & Mutation Effects

hg38 • Region Span ~76.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to COX19 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 16

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001031617.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			14 clinvar	2 clinvar		16
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	15	2	0	17

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001031617.3	RefSeq	NP_001026788.1	3	MANE Select
ENST00000344111.4	Ensembl	ENSP00000342015.3	3	MANE Select
ENST00000457254.5	Ensembl	ENSP00000413423.1	4	Standard
ENST00001091656.1	Ensembl	ENSP00000761462.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Thermogenesis - Homo sapiens (human)
Metabolism of proteins
Mitochondrial protein import

Biological Process

cellular copper ion homeostasis
mitochondrial respiratory chain complex IV assembly

Molecular Function

protein binding

Cellular Component

mitochondrion
mitochondrial intermembrane space
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000344111
Coding exons: 3
Length: 76821
Individuals with no LoFs: 124971
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 124976
p: 0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.02	62	43.1	1.44	0.00000185	600
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000039	0.000035	rare
South Asian	0.000034	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.0885

Intolerance Scores

LoFtool: 0.593
RVIS EVS: 0.37
RVIS percentile EVS: 74.95

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): K
Indispensability pred.: N
Indispensability score: 0.341

Gene Damage Prediction

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