NDUFB11

NADH:ubiquinone oxidoreductase subunit B11, the group of NADH:ubiquinone oxidoreductase supernumerary subunits

Basic information

Region (hg38): X:47142071-47145466

Links

ENSG00000147123 ∙ NCBI:54539 ∙ OMIM:300403 ∙ HGNC:20372 ∙ Uniprot:Q9NX14 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• linear skin defects with multiple congenital anomalies (Supportive), mode of inheritance: XL
• linear skin defects with multiple congenital anomalies 3 (Strong), mode of inheritance: XL
• mitochondrial complex I deficiency, nuclear type 30 (Strong), mode of inheritance: XL
• mitochondrial disease (Definitive), mode of inheritance: XL
• linear skin defects with multiple congenital anomalies 3 (Strong), 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 3	XL	Cardiovascular	Among other findings, individuals have been described with early-onset cardiomyopathy, and awareness may allow prompt awareness and management	Biochemical; Cardiovascular; Dermatologic; Neurologic	25772934; 26741492
Cardiac transplantation has been described

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NDUFB11 gene.

• not_provided (52 variants)
• Inborn_genetic_diseases (15 variants)
• Linear_skin_defects_with_multiple_congenital_anomalies_3 (8 variants)
• NDUFB11-related_disorders (6 variants)
• Mitochondrial_complex_I_deficiency,_nuclear_type_30 (6 variants)
• not_specified (3 variants)
• Linear_skin_defects_with_multiple_congenital_anomalies_1 (2 variants)
• Neurodevelopmental_disorder (1 variants)
• Histiocytoid_cardiomyopathy (1 variants)
• Intellectual_disability (1 variants)
• Mitochondrial_complex_I_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 NDUFB11 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001135998.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				14		14
missense		2	31	5	2	40
nonsense	1	1				2
start loss			1			1
frameshift	1	2				3
splice donor/acceptor (+/-2bp)		1		1		2
Total	2	6	32	20	2

Highest pathogenic variant AF is 0.000015485304

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NDUFB11	protein_coding	protein_coding	ENST00000276062	3	3289

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.804	0.192	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.513	54	65.7	0.822	0.00000506	1046
Missense in Polyphen		14	23.13	0.60527		388
Synonymous	-0.292	30	28.0	1.07	0.00000227	333
Loss of Function	2.15	0	5.39	0.00	4.86e-7	71

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: Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), that is believed not to be involved in catalysis. Complex I functions in the transfer of electrons from NADH to the respiratory chain. The immediate electron acceptor for the enzyme is believed to be ubiquinone. {ECO:0000269|PubMed:27626371}.
• Disease: DISEASE: Mitochondrial complex I deficiency (MT-C1D) [MIM:252010]: A disorder of the mitochondrial respiratory chain that causes a wide range of clinical manifestations from lethal neonatal disease to adult-onset neurodegenerative disorders. Phenotypes include macrocephaly with progressive leukodystrophy, non-specific encephalopathy, cardiomyopathy, myopathy, liver disease, Leigh syndrome, Leber hereditary optic neuropathy, and some forms of Parkinson disease. {ECO:0000269|PubMed:26741492}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Retrograde endocannabinoid signaling - 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);Respiratory electron transport;The citric acid (TCA) cycle and respiratory electron transport;Metabolism;Complex I biogenesis;Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. (Consensus)

Recessive Scores

• pRec: 0.335

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.105
• hipred: N
• hipred_score: 0.145
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.613

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ndufb11

Zebrafish Information Network

• Gene name: ndufb11
• Affected structure: trunk vasculature
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: mitochondrial respiratory chain complex I assembly;oxidation-reduction process
• Cellular component: mitochondrion;mitochondrial inner membrane;mitochondrial respiratory chain complex I;integral component of membrane
• Molecular function: protein binding