NDUFB11

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

Basic information

Region (hg38): X:47142070-47145466

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 1 (Strong), mode of inheritance: XLD
• 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
• linear skin defects with multiple congenital anomalies 1 (Strong), mode of inheritance: XL
• mitochondrial complex 1 deficiency, nuclear type 30 (Strong), mode of inheritance: XL
• mitochondrial disease (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 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 (44 variants)
• Linear skin defects with multiple congenital anomalies 3 (5 variants)
• Inborn genetic diseases (5 variants)
• Mitochondrial complex 1 deficiency, nuclear type 30 (4 variants)
• not specified (2 variants)
• NDUFB11-related condition (2 variants)
• Linear skin defects with multiple congenital anomalies 1;Linear skin defects with multiple congenital anomalies 3;Mitochondrial complex I deficiency, nuclear type 1 (1 variants)
• Histiocytoid cardiomyopathy (1 variants)
• Neurodevelopmental disorder (1 variants)
• Linear skin defects with multiple congenital anomalies 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.

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				4		4
missense		2	18	9	2	31
nonsense	1	1				2
start loss			1			1
frameshift		2				2
inframe indel	1					1
splice donor/acceptor (+/-2bp)		1		1		2
splice region					1	1
non coding			3	5	2	10
Total	2	6	22	19	4

Variants in NDUFB11

This is a list of pathogenic ClinVar variants found in the NDUFB11 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-47142212-C-T			Benign (Jul 09, 2018)
X-47142334-G-T			Uncertain significance (Jan 27, 2022)
X-47142352-C-G		NDUFB11-related disorder	Uncertain significance (May 15, 2023)
X-47142352-C-T		Mitochondrial complex 1 deficiency, nuclear type 30	Uncertain significance (Jun 13, 2019)
X-47142353-G-A			Likely benign (Aug 28, 2022)
X-47142363-G-A		not specified	Benign (May 04, 2022)
X-47142364-A-C			Conflicting classifications of pathogenicity (Aug 23, 2023)
X-47142371-G-C			Uncertain significance (Dec 26, 2022)
X-47142375-G-A			Uncertain significance (Dec 01, 2022)
X-47142389-C-T			Likely benign (Mar 30, 2018)
X-47142394-G-A		Linear skin defects with multiple congenital anomalies 3 • NDUFB11-related disorder	Likely pathogenic (Aug 08, 2023)
X-47142406-GC-G		Linear skin defects with multiple congenital anomalies 3	Pathogenic (Apr 02, 2015)
X-47142418-C-T		Mitochondrial complex 1 deficiency, nuclear type 30 • Linear skin defects with multiple congenital anomalies 3	Pathogenic/Likely pathogenic (Oct 05, 2023)
X-47142419-G-A			Likely benign (May 29, 2023)
X-47142420-C-T		Linear skin defects with multiple congenital anomalies 1	Uncertain significance (Apr 27, 2019)
X-47142421-G-A			Uncertain significance (Sep 10, 2021)
X-47142424-G-A			Uncertain significance (Mar 08, 2023)
X-47142438-A-C		Inborn genetic diseases	Uncertain significance (Oct 16, 2023)
X-47142576-C-T			Likely benign (Apr 12, 2023)
X-47142581-T-C			Uncertain significance (Dec 04, 2022)
X-47142592-C-A			Likely benign (Aug 31, 2022)
X-47142592-C-T			Benign/Likely benign (Dec 26, 2023)
X-47142593-G-A			Uncertain significance (Oct 13, 2023)
X-47142597-T-C			Uncertain significance (Oct 13, 2023)
X-47142603-A-G			Uncertain significance (Oct 13, 2022)

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