ATP5F1B

ATP synthase F1 subunit beta, the group of Mitochondrial complex V: ATP synthase subunits|Small nucleolar RNA protein coding host genes|ATPase F1/V1 alpha/A and beta/B subunit family

Basic information

Region (hg38): 12:56638175-56645984

Previous symbols: [ "ATPSB", "ATP5B" ]

Links

ENSG00000110955 ∙ NCBI:506 ∙ OMIM:102910 ∙ HGNC:830 ∙ Uniprot:P06576 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hypermetabolism due to uncoupled mitochondrial oxidative phosphorylation 2 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hypermetabolism due to uncoupled mitochondrial oxidative phosphorylation 2	AD	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; Neurologic	36239646

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP5F1B gene.

• Hypermetabolism due to Defect in Mitochondrial Coupling (1 variants)
• Hypermetabolism due to uncoupled mitochondrial oxidative phosphorylation 2 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP5F1B 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						0
missense	1		23	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	0	23	1	0

Variants in ATP5F1B

This is a list of pathogenic ClinVar variants found in the ATP5F1B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-56638333-T-C		not specified	Uncertain significance (Dec 31, 2024)
12-56638338-T-A		not specified	Uncertain significance (Dec 03, 2021)
12-56638355-C-A		not specified	Uncertain significance (Feb 26, 2025)
12-56638378-G-T		not specified	Uncertain significance (Feb 17, 2024)
12-56638417-T-C		not specified	Uncertain significance (Jan 23, 2025)
12-56639116-C-A		not specified	Uncertain significance (Nov 15, 2021)
12-56639215-T-C		not specified	Uncertain significance (Oct 04, 2022)
12-56639251-C-A		not specified	Uncertain significance (Feb 13, 2024)
12-56640189-T-C		not specified	Uncertain significance (Oct 29, 2024)
12-56642479-C-G			Uncertain significance (Sep 01, 2024)
12-56642528-A-G		Hypermetabolism due to uncoupled mitochondrial oxidative phosphorylation 2 • Hypermetabolism due to Defect in Mitochondrial Coupling	Pathogenic (Jul 29, 2022)
12-56643443-A-G		not specified	Uncertain significance (Oct 21, 2021)
12-56643950-G-C		not specified	Uncertain significance (Mar 28, 2023)
12-56644872-T-C		not specified	Uncertain significance (Sep 16, 2021)
12-56644949-C-G		not specified	Uncertain significance (Oct 08, 2024)
12-56644952-T-A		not specified	Uncertain significance (Mar 01, 2024)
12-56645239-G-A		not specified	Uncertain significance (Aug 02, 2021)
12-56645254-T-A		not specified	Uncertain significance (Jul 14, 2021)
12-56645297-G-A		not specified	Uncertain significance (Feb 12, 2025)
12-56645306-C-T		not specified	Uncertain significance (Feb 27, 2023)
12-56645315-C-T		not specified	Uncertain significance (Feb 13, 2025)
12-56645323-G-A		not specified	Uncertain significance (Dec 10, 2024)
12-56645329-G-A		not specified	Uncertain significance (Dec 19, 2024)
12-56645344-T-C		not specified	Uncertain significance (Jan 19, 2022)
12-56645855-G-C		not specified	Uncertain significance (Dec 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP5F1B	protein_coding	protein_coding	ENST00000262030	10	7840

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.977	0.0232	125741	0	7	125748	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.17	150	306	0.490	0.0000156	3388
Missense in Polyphen		30	129.28	0.23205		1454
Synonymous	1.91	92	118	0.776	0.00000589	1145
Loss of Function	3.77	2	20.4	0.0982	9.49e-7	253

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core, and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Subunits alpha and beta form the catalytic core in F(1). Rotation of the central stalk against the surrounding alpha(3)beta(3) subunits leads to hydrolysis of ATP in three separate catalytic sites on the beta subunits.
• Pathway: Alzheimer,s disease - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);Thermogenesis - Homo sapiens (human);Doxorubicin Pathway (Cardiomyocyte Cell), Pharmacodynamics;Oxidative phosphorylation - Homo sapiens (human);Parkinson,s disease - Homo sapiens (human);Mitochondrial Electron Transport Chain;Electron Transport Chain;Mitochondrial biogenesis;Oxidative phosphorylation;adenosine ribonucleotides <i>de novo</i> biosynthesis;Metabolism of proteins;Formation of ATP by chemiosmotic coupling;The citric acid (TCA) cycle and respiratory electron transport;Purine metabolism;Metabolism;superpathway of purine nucleotide salvage;Mitochondrial protein import;Transcriptional activation of mitochondrial biogenesis;Cristae formation;Mitochondrial biogenesis;Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.;purine nucleotides <i>de novo</i> biosynthesis;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.705

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.92

Haploinsufficiency Scores

• pHI: 0.853
• hipred: Y
• hipred_score: 0.739
• ghis: 0.547

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Atp5b
• Phenotype: skeleton phenotype; limbs/digits/tail phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: angiogenesis;osteoblast differentiation;generation of precursor metabolites and energy;lipid metabolic process;ATP biosynthetic process;negative regulation of cell adhesion involved in substrate-bound cell migration;mitochondrion organization;cristae formation;mitochondrial ATP synthesis coupled proton transport;positive regulation of blood vessel endothelial cell migration;regulation of intracellular pH;cellular response to interleukin-7;ATP hydrolysis coupled cation transmembrane transport;proton transmembrane transport
• Cellular component: nucleus;mitochondrion;mitochondrial proton-transporting ATP synthase complex;mitochondrial proton-transporting ATP synthase, catalytic core;mitochondrial matrix;plasma membrane;cell surface;membrane;mitochondrial membrane;mitochondrial nucleoid;myelin sheath;proton-transporting ATP synthase complex;extracellular exosome
• Molecular function: transporter activity;protein binding;ATP binding;ATPase activity;transmembrane transporter activity;MHC class I protein binding;angiostatin binding;proton-transporting ATP synthase activity, rotational mechanism;proton-transporting ATPase activity, rotational mechanism