ATP5PD

ATP synthase peripheral stalk subunit d, the group of Mitochondrial complex V: ATP synthase subunits

Basic information

Region (hg38): 17:75038862-75046985

Previous symbols: [ "ATP5H" ]

Links

ENSG00000167863 ∙ NCBI:10476 ∙ OMIM:618121 ∙ HGNC:845 ∙ Uniprot:O75947 ∙ 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 ATP5PD gene.

• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ATP5PD 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in ATP5PD

This is a list of pathogenic ClinVar variants found in the ATP5PD region.

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

Position	Type	Phenotype	Significance	ClinVar
17-75039234-G-A		not specified	Uncertain significance (Aug 15, 2023)
17-75040126-T-C		not specified	Uncertain significance (Oct 06, 2022)
17-75040148-C-A		not specified	Uncertain significance (Aug 02, 2021)
17-75042246-T-C		not specified	Uncertain significance (Apr 12, 2022)
17-75042578-T-C		not specified	Uncertain significance (Dec 02, 2022)
17-75042593-T-C		not specified	Uncertain significance (May 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ATP5PD	protein_coding	protein_coding	ENST00000301587	5	8123

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000460	0.681	125654	0	93	125747	0.000370

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.743	65	84.2	0.772	0.00000394	1066
Missense in Polyphen		20	36.205	0.55241		496
Synonymous	0.423	28	31.0	0.903	0.00000166	279
Loss of Function	0.791	6	8.49	0.707	3.57e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000998	0.000998
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000440	0.000440
Middle Eastern	0.00	0.00
South Asian	0.000163	0.000163
Other	0.000815	0.000815

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);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: 0.131

Intolerance Scores

• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.0888
• hipred: Y
• hipred_score: 0.632
• ghis: 0.614

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Atp5h

Gene ontology

• Biological process: ATP biosynthetic process;ATP synthesis coupled proton transport;cristae formation;mitochondrial ATP synthesis coupled proton transport;ATP hydrolysis coupled cation transmembrane transport
• Cellular component: mitochondrial proton-transporting ATP synthase, stator stalk;nucleoplasm;mitochondrion;mitochondrial inner membrane;mitochondrial proton-transporting ATP synthase complex;myelin sheath
• Molecular function: ATPase activity;transmembrane transporter activity;proton-transporting ATP synthase activity, rotational mechanism