COX7B

cytochrome c oxidase subunit 7B, the group of Mitochondrial complex IV: cytochrome c oxidase subunits

Basic information

Region (hg38): X:77899440-77907376

Links

ENSG00000131174 ∙ NCBI:1349 ∙ OMIM:300885 ∙ HGNC:2291 ∙ Uniprot:P24311 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• linear skin defects with multiple congenital anomalies 2 (Definitive), mode of inheritance: XLD
• linear skin defects with multiple congenital anomalies 2 (Strong), mode of inheritance: XL
• linear skin defects with multiple congenital anomalies (Supportive), mode of inheritance: XL
• linear skin defects with multiple congenital anomalies 2 (Definitive), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Linear skin defects with multiple congenital anomalies 2	XL	Cardiovascular	The condition can involve congenital cardiac anomalies, and awareness may allow early management	Cardiovascular; Craniofacial; Dermatologic; Musculoskeletal; Neurologic; Ophthalmologic; Renal	9747372; 23122588

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the COX7B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the COX7B 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				3		3
missense			8	1	1	10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region		1		1		2
non coding				8	1	9
Total	0	0	8	12	2

Variants in COX7B

This is a list of pathogenic ClinVar variants found in the COX7B region.

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

Position	Type	Phenotype	Significance	ClinVar
X-77899512-A-G		not specified	Likely benign (Jul 18, 2017)
X-77899560-C-G			Uncertain significance (Mar 03, 2017)
X-77899570-A-G		Inborn genetic diseases	Likely benign (Aug 20, 2024)
X-77899574-C-A		Inborn genetic diseases	Conflicting classifications of pathogenicity (Aug 20, 2024)
X-77899598-G-C			Likely pathogenic (Feb 03, 2016)
X-77902417-A-G			Likely benign (Sep 11, 2018)
X-77902629-C-T			Benign (Jul 17, 2023)
X-77902630-G-A			Likely benign (Mar 03, 2023)
X-77902638-G-A			Likely benign (Sep 05, 2022)
X-77902641-A-G		Linear skin defects with multiple congenital anomalies 2	Pathogenic (Nov 02, 2012)
X-77902650-C-A		not specified	Benign (Jan 08, 2024)
X-77902657-C-T		Linear skin defects with multiple congenital anomalies 2	Pathogenic (Nov 02, 2012)
X-77902676-G-A			Uncertain significance (May 29, 2023)
X-77902687-C-T		Inborn genetic diseases	Likely benign (Jan 24, 2024)
X-77902688-G-A		Linear skin defects with multiple congenital anomalies 2	Uncertain significance (Jan 11, 2024)
X-77902709-A-G		Inborn genetic diseases	Conflicting classifications of pathogenicity (Oct 19, 2024)
X-77902742-C-T			Uncertain significance (Sep 30, 2023)
X-77902762-A-G		Inborn genetic diseases	Conflicting classifications of pathogenicity (Jan 08, 2024)
X-77902777-A-G		not specified • COX7B-related disorder	Benign (Sep 05, 2022)
X-77902780-G-A			Likely benign (Jul 09, 2023)
X-77902939-T-C			Likely benign (Sep 02, 2019)
X-77903028-G-GT			Likely benign (Oct 21, 2019)
X-77905187-G-T			Uncertain significance (Sep 28, 2022)
X-77905198-C-T			Likely benign (Apr 06, 2023)
X-77905212-AC-A		Linear skin defects with multiple congenital anomalies 2	Pathogenic (Nov 02, 2012)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
COX7B	protein_coding	protein_coding	ENST00000481445	3	7936

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.675	0.307	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.424	25	31.7	0.788	0.00000240	521
Missense in Polyphen		2	6.7873	0.29467		159
Synonymous	-0.763	14	10.8	1.30	8.27e-7	149
Loss of Function	1.77	0	3.66	0.00	2.87e-7	49

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

• Function: FUNCTION: This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. Plays a role in proper central nervous system (CNS) development in vertebrates. {ECO:0000269|PubMed:23122588}.
• Disease: DISEASE: Linear skin defects with multiple congenital anomalies 2 (LSDMCA2) [MIM:300887]: A distinct form of aplasia cutis congenita presenting as multiple linear skin defects on the face and neck associated with poor growth, microcephaly, and facial dysmorphism. Additional features include intellectual disability, nail dystrophy, short stature and cardiac abnormalities. {ECO:0000269|PubMed:23122588}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Cardiac muscle contraction - Homo sapiens (human);Non-alcoholic fatty liver disease (NAFLD) - Homo sapiens (human);Alzheimer,s disease - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Oxidative phosphorylation - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);Electron Transport Chain;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Respiratory electron transport;The citric acid (TCA) cycle and respiratory electron transport;Metabolism;TP53 Regulates Metabolic Genes;Transcriptional Regulation by TP53;Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. (Consensus)

Recessive Scores

• pRec: 0.0840

Intolerance Scores

• rvis_EVS: 0.28
• rvis_percentile_EVS: 70.87

Haploinsufficiency Scores

• pHI: 0.0693
• hipred: N
• hipred_score: 0.432
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.819

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cox7b
• Phenotype: embryo phenotype

Gene ontology

• Biological process: central nervous system development;electron transport chain;proton transmembrane transport
• Cellular component: mitochondrial inner membrane;mitochondrial respirasome;integral component of membrane;respiratory chain complex IV
• Molecular function: cytochrome-c oxidase activity