PET100

PET100 cytochrome c oxidase chaperone, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 19:7629788-7631956

Previous symbols: [ "C19orf79" ]

Links

ENSG00000229833 ∙ NCBI:100131801 ∙ OMIM:614770 ∙ HGNC:40038 ∙ Uniprot:P0DJ07 ∙ 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 12 (Strong), mode of inheritance: AR
• Leigh syndrome with leukodystrophy (Supportive), mode of inheritance: AR
• cytochrome-c oxidase deficiency disease (Strong), 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 12	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; Ophthalmologic	24462369

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PET100 gene.

• not provided (5 variants)
• Mitochondrial complex 4 deficiency, nuclear type 12 (2 variants)
• Mitochondrial complex IV deficiency, nuclear type 1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PET100 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			1	9		10
missense			12	2	1	15
nonsense	2	1	1			4
start loss	3					3
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)		4	1			5
splice region			1	4		5
non coding			1	32	6	39
Total	5	5	17	43	7

Highest pathogenic variant AF is 0.00000658

Variants in PET100

This is a list of pathogenic ClinVar variants found in the PET100 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-7629815-G-C		not specified	Likely benign (Jul 01, 2016)
19-7629831-G-A		not specified	Likely benign (Aug 04, 2017)
19-7629834-A-G		Mitochondrial complex 4 deficiency, nuclear type 12	Pathogenic (Jul 28, 2023)
19-7629834-A-T			Pathogenic (Nov 23, 2021)
19-7629836-G-C		Mitochondrial complex IV deficiency, nuclear type 1 • Mitochondrial complex 4 deficiency, nuclear type 12 • PET100-related disorder	Pathogenic (Aug 05, 2023)
19-7629851-G-A			Likely benign (Oct 14, 2023)
19-7629855-TTTCGGGTCA-T			Likely pathogenic (Apr 25, 2023)
19-7629870-C-T			Likely benign (Sep 20, 2023)
19-7629871-A-G			Likely benign (Jan 22, 2024)
19-7629874-G-A			Likely benign (Feb 15, 2023)
19-7629875-G-A			Likely benign (Dec 20, 2022)
19-7629875-G-C			Likely benign (Jun 11, 2023)
19-7630380-G-C			Benign (Jun 19, 2018)
19-7630450-A-G			Benign (Jun 23, 2018)
19-7630555-C-T			Likely benign (Aug 01, 2023)
19-7630559-C-G			Likely benign (May 25, 2023)
19-7630571-A-G			Likely pathogenic (Oct 22, 2023)
19-7630584-C-A			Pathogenic (Jul 10, 2023)
19-7630611-G-A			Pathogenic (Mar 22, 2023)
19-7630619-A-G		PET100-related disorder • Mitochondrial complex 4 deficiency, nuclear type 12	Conflicting classifications of pathogenicity (Jan 31, 2024)
19-7630627-G-A		PET100-related disorder	Benign/Likely benign (Jan 31, 2024)
19-7630627-G-C			Uncertain significance (Sep 01, 2022)
19-7630660-G-A			Likely pathogenic (Jan 05, 2024)
19-7630663-G-A		PET100-related disorder	Uncertain significance (Dec 02, 2021)
19-7630666-A-G			Likely benign (Mar 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PET100	protein_coding	protein_coding	ENST00000594797	4	2220

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000359	0.397	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.242	38	42.4	0.895	0.00000272	477
Missense in Polyphen		0	0.88583	0		12
Synonymous	1.37	8	14.7	0.544	9.41e-7	122
Loss of Function	-0.0597	5	4.86	1.03	2.08e-7	54

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.63
• rvis_percentile_EVS: 83.59

Haploinsufficiency Scores

• ghis: 0.486

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pet100

Gene ontology

• Biological process: mitochondrial respiratory chain complex IV assembly
• Cellular component: integral component of mitochondrial inner membrane
• Molecular function: unfolded protein binding