COA7

cytochrome c oxidase assembly factor 7, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 1:52684449-52698347

Previous symbols: [ "C1orf163", "SELRC1" ]

Links

ENSG00000162377 ∙ NCBI:65260 ∙ OMIM:615623 ∙ HGNC:25716 ∙ Uniprot:Q96BR5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 3 (Moderate), mode of inheritance: AR
• spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 3 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 3	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	Neurologic	27683825; 29718187

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COA7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COA7 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				12		12
missense		1	23	1	1	26
nonsense						0
start loss						0
frameshift		2				2
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region			1	1		2
non coding				3	4	7
Total	0	4	23	16	5

Variants in COA7

This is a list of pathogenic ClinVar variants found in the COA7 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-52687721-T-C			Likely benign (Dec 06, 2023)
1-52687758-C-G		Inborn genetic diseases	Uncertain significance (Jan 15, 2024)
1-52687760-T-C			Benign (Feb 03, 2025)
1-52687763-T-A			Uncertain significance (Aug 22, 2022)
1-52687770-G-C			Uncertain significance (Oct 15, 2024)
1-52687795-G-A			Likely benign (Mar 20, 2023)
1-52687839-T-C			Uncertain significance (Mar 11, 2023)
1-52687842-G-A			Likely pathogenic (Jan 01, 2019)
1-52687846-G-A			Likely benign (Sep 20, 2023)
1-52687860-C-T			Uncertain significance (Dec 01, 2023)
1-52687865-A-ATATGACCCAGG			Likely pathogenic (Jan 01, 2019)
1-52687890-T-C		Inborn genetic diseases	Uncertain significance (Sep 03, 2024)
1-52687960-G-A			Likely benign (Oct 17, 2024)
1-52687969-A-G		COA7-related disorder	Likely benign (Jun 29, 2024)
1-52687970-C-A		Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 3	Pathogenic (Apr 15, 2019)
1-52687984-AC-A		Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 3	Pathogenic (Apr 15, 2019)
1-52688006-T-C		Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 3	Pathogenic (Apr 18, 2019)
1-52688009-T-C			Uncertain significance (Dec 01, 2023)
1-52688070-G-A			Uncertain significance (Jun 26, 2022)
1-52688076-C-T			Uncertain significance (Aug 28, 2023)
1-52688077-G-A			Likely benign (Jun 03, 2024)
1-52688086-T-C			Likely benign (Oct 29, 2024)
1-52688119-C-T			Likely benign (Oct 05, 2022)
1-52688141-G-A			Uncertain significance (Dec 01, 2021)
1-52688165-C-T		Inborn genetic diseases	Uncertain significance (Jan 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COA7	protein_coding	protein_coding	ENST00000371538	3	11531

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0597	0.875	125735	0	12	125747	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.672	106	127	0.832	0.00000626	1533
Missense in Polyphen		40	41.299	0.96855		506
Synonymous	0.0262	50	50.2	0.995	0.00000256	412
Loss of Function	1.55	3	7.60	0.395	3.17e-7	113

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000179	0.000177
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for assembly of mitochondrial respiratory chain complex I and complex IV. {ECO:0000269|PubMed:24333015}.
• Pathway: Thermogenesis - Homo sapiens (human) (Consensus)

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.98

Haploinsufficiency Scores

• pHI: 0.365
• hipred: N
• hipred_score: 0.240
• ghis: 0.484

Essentials

• 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: Coa7

Gene ontology

• Cellular component: nucleus;mitochondrion;mitochondrial intermembrane space