ATP5PB

ATP synthase peripheral stalk-membrane subunit b, the group of Mitochondrial complex V: ATP synthase subunits

Basic information

Region (hg38): 1:111448864-111462773

Previous symbols: [ "ATP5F1" ]

Links

ENSG00000116459 ∙ NCBI:515 ∙ OMIM:603270 ∙ HGNC:840 ∙ Uniprot:P24539 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ATP5PB gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP5PB 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in ATP5PB

This is a list of pathogenic ClinVar variants found in the ATP5PB region.

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

Position	Type	Phenotype	Significance	ClinVar
1-111449144-A-C		not specified	Uncertain significance (Oct 03, 2023)
1-111449147-G-A		not specified	Uncertain significance (Mar 30, 2024)
1-111449840-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-111449843-C-T		not specified	Uncertain significance (Jul 13, 2021)
1-111454212-G-T		not specified	Uncertain significance (Sep 21, 2023)
1-111454280-A-C		not specified	Uncertain significance (Oct 12, 2021)
1-111456094-G-A		not specified	Uncertain significance (Dec 01, 2022)
1-111456151-G-A		not specified	Uncertain significance (Aug 02, 2022)
1-111459472-G-A		not specified	Uncertain significance (Sep 30, 2021)
1-111459530-G-A		not specified	Uncertain significance (Jul 25, 2023)
1-111459542-A-G		not specified	Uncertain significance (Dec 13, 2021)
1-111459565-C-G		not specified	Uncertain significance (Aug 30, 2021)
1-111459580-G-A		not specified	Uncertain significance (Feb 15, 2023)
1-111459618-A-C		not specified	Uncertain significance (Aug 12, 2021)
1-111460927-C-G		not specified	Uncertain significance (Mar 28, 2022)
1-111460990-T-C		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP5PB	protein_coding	protein_coding	ENST00000369722	7	13910

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00153	0.971	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00502	145	145	1.00	0.00000776	1651
Missense in Polyphen		36	42.521	0.84663		575
Synonymous	-0.392	56	52.4	1.07	0.00000290	503
Loss of Function	1.94	7	15.2	0.462	8.07e-7	168

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000257	0.000251
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000580	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000273	0.0000264
Middle Eastern	0.0000580	0.0000544
South Asian	0.0000980	0.0000980
Other	0.000165	0.000163

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. Part of the complex F(0) domain and the peripheric stalk, which acts as a stator to hold the catalytic alpha(3)beta(3) subcomplex and subunit a/ATP6 static relative to the rotary elements.
• 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;Oxidative phosphorylation;adenosine ribonucleotides <i>de novo</i> biosynthesis;Formation of ATP by chemiosmotic coupling;The citric acid (TCA) cycle and respiratory electron transport;Purine metabolism;Metabolism;superpathway of purine nucleotide salvage;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: 0.106

Intolerance Scores

• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.416
• hipred: Y
• hipred_score: 0.560
• ghis: 0.595

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Atp5f1
• Phenotype: immune system 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); hematopoietic system phenotype

Zebrafish Information Network

• Gene name: atp5pb
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: viability

Gene ontology

• Biological process: ATP biosynthetic process;ATP synthesis coupled proton transport;substantia nigra development;cristae formation;mitochondrial ATP synthesis coupled proton transport;ATP hydrolysis coupled cation transmembrane transport
• Cellular component: mitochondrial proton-transporting ATP synthase complex, coupling factor F(o);nucleus;nucleoplasm;mitochondrion;mitochondrial inner membrane;mitochondrial proton-transporting ATP synthase complex;mitochondrial matrix;membrane;myelin sheath
• Molecular function: protein binding;ATPase activity;transmembrane transporter activity;proton-transporting ATP synthase activity, rotational mechanism