PDSS1 (decaprenyl diphosphate synthase subunit 1)

Gene

• Entrez ID: 23590
• Gene name: Decaprenyl diphosphate synthase subunit 1
• Gene symbol: PDSS1
• Synonyms (NCBI Gene): COQ1, COQ10D2, COQ1A, DPS, SPS, TPRT, TPT, TPT 1, hDPS1
• Chromosome: 10
• Chromosome location: 10p12.1
• Summary: The protein encoded by this gene is an enzyme that elongates the prenyl side-chain of coenzyme Q, or ubiquinone, one of the key elements in the respiratory chain. The gene product catalyzes the formation of all trans-polyprenyl pyrophosphates from isopent

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs119463988	T>A,G	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant, intron variant
rs863224162	G>T	Likely-pathogenic	Intron variant, upstream transcript variant, genic upstream transcript variant
rs863224163	C>-	Pathogenic	Non coding transcript variant, coding sequence variant, intron variant, frameshift variant
rs1057519353	->T	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT019328	hsa-miR-148b-3p	Microarray	17612493
MIRT022672	hsa-miR-124-3p	Microarray	18668037
MIRT027634	hsa-miR-98-5p	Microarray	19088304
MIRT044710	hsa-miR-320a	CLASH	23622248
MIRT044367	hsa-miR-106b-5p	CLASH	23622248
MIRT1223383	hsa-miR-132	CLIP-seq
MIRT1223384	hsa-miR-140-3p	CLIP-seq
MIRT1223385	hsa-miR-212	CLIP-seq
MIRT1223386	hsa-miR-22	CLIP-seq
MIRT1223387	hsa-miR-30a	CLIP-seq
MIRT1223388	hsa-miR-30b	CLIP-seq
MIRT1223389	hsa-miR-30c	CLIP-seq
MIRT1223390	hsa-miR-30d	CLIP-seq
MIRT1223391	hsa-miR-30e	CLIP-seq
MIRT1223392	hsa-miR-3133	CLIP-seq
MIRT1223393	hsa-miR-3201	CLIP-seq
MIRT1223394	hsa-miR-3622a-5p	CLIP-seq
MIRT1223395	hsa-miR-3691-5p	CLIP-seq
MIRT1223396	hsa-miR-3692	CLIP-seq
MIRT1223397	hsa-miR-4423-3p	CLIP-seq
MIRT1223398	hsa-miR-4490	CLIP-seq
MIRT1223399	hsa-miR-4491	CLIP-seq
MIRT1223400	hsa-miR-4657	CLIP-seq
MIRT1223401	hsa-miR-4662a-3p	CLIP-seq
MIRT1223402	hsa-miR-4752	CLIP-seq
MIRT1223403	hsa-miR-4774-5p	CLIP-seq
MIRT1223404	hsa-miR-4791	CLIP-seq
MIRT1223405	hsa-miR-622	CLIP-seq
MIRT1223406	hsa-miR-630	CLIP-seq
MIRT1223386	hsa-miR-22	CLIP-seq
MIRT1223394	hsa-miR-3622a-5p	CLIP-seq
MIRT1223397	hsa-miR-4423-3p	CLIP-seq
MIRT1223398	hsa-miR-4490	CLIP-seq
MIRT1223401	hsa-miR-4662a-3p	CLIP-seq
MIRT1223403	hsa-miR-4774-5p	CLIP-seq
MIRT1223405	hsa-miR-622	CLIP-seq
MIRT1223406	hsa-miR-630	CLIP-seq
MIRT1223386	hsa-miR-22	CLIP-seq
MIRT1223394	hsa-miR-3622a-5p	CLIP-seq
MIRT1223396	hsa-miR-3692	CLIP-seq
MIRT1223397	hsa-miR-4423-3p	CLIP-seq
MIRT1223398	hsa-miR-4490	CLIP-seq
MIRT1223401	hsa-miR-4662a-3p	CLIP-seq
MIRT1223403	hsa-miR-4774-5p	CLIP-seq
MIRT2292999	hsa-miR-520g	CLIP-seq
MIRT2293000	hsa-miR-520h	CLIP-seq
MIRT1223405	hsa-miR-622	CLIP-seq
MIRT1223406	hsa-miR-630	CLIP-seq
MIRT1223386	hsa-miR-22	CLIP-seq
MIRT1223394	hsa-miR-3622a-5p	CLIP-seq
MIRT1223397	hsa-miR-4423-3p	CLIP-seq
MIRT1223398	hsa-miR-4490	CLIP-seq
MIRT1223401	hsa-miR-4662a-3p	CLIP-seq
MIRT1223403	hsa-miR-4774-5p	CLIP-seq
MIRT1223405	hsa-miR-622	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004659	Function	Prenyltransferase activity	IBA
GO:0004659	Function	Prenyltransferase activity	IEA
GO:0005515	Function	Protein binding	IPI	16262699
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006744	Process	Ubiquinone biosynthetic process	IBA
GO:0006744	Process	Ubiquinone biosynthetic process	IDA	16262699
GO:0006744	Process	Ubiquinone biosynthetic process	IEA
GO:0008299	Process	Isoprenoid biosynthetic process	IBA
GO:0008299	Process	Isoprenoid biosynthetic process	IDA	16262699
GO:0008299	Process	Isoprenoid biosynthetic process	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0032476	Component	Polyprenyl diphosphate synthase complex	IBA
GO:0032478	Component	Heterotetrameric polyprenyl diphosphate synthase complex	IDA	16262699
GO:0032478	Component	Heterotetrameric polyprenyl diphosphate synthase complex	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0046982	Function	Protein heterodimerization activity	IEA
GO:0052923	Function	All-trans-nonaprenyl-diphosphate synthase (geranyl-diphosphate specific) activity	IEA
GO:0097269	Function	All-trans-decaprenyl-diphosphate synthase activity	IDA	16262699
GO:0097269	Function	All-trans-decaprenyl-diphosphate synthase activity	IEA
GO:0110142	Component	Ubiquinone biosynthesis complex	IEA
GO:1990234	Component	Transferase complex	IEA

Other IDs

• MIM: 607429
• HGNC: 17759
• e!Ensembl: ENSG00000148459

Protein

• UniProt ID: Q5T2R2
• Protein name: All trans-polyprenyl-diphosphate synthase PDSS1 (All-trans-decaprenyl-diphosphate synthase subunit 1) (EC 2.5.1.91) (Decaprenyl pyrophosphate synthase subunit 1) (Decaprenyl-diphosphate synthase subunit 1) (Solanesyl-diphosphate synthase subunit 1) (Trans
• Protein function: Heterotetrameric enzyme that catalyzes the condensation of farnesyl diphosphate (FPP), which acts as a primer, and isopentenyl diphosphate (IPP) to produce prenyl diphosphates of varying chain lengths and participates in the determination of the
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00348	polyprenyl_synt	118 → 367	Polyprenyl synthetase	Domain

• Sequence:

  MASRWWRWRRGCSWKPAARSPGPGSPGRAGPLGPSAAAEVRAQVHRRKGLDLSQIPYINL
  VKHLTSACPNVCRISRFHHTTPDSKTHSGEKYTDPFKLGWRDLKGLYEDIRKELLISTSE
  LKEMSEYYFDGKGKAFRPIIVALMARACNIHHNNSRHVQASQRAIALIAEMIHTASLVHD
  DVIDDASSRRGKHTVNKIWGEKKAVLAGDLILSAASIALARIGNTTVISILTQVIEDLVR
  GEFLQLGSKENENERFAHYLEKTFKKTASLIANSCKAVSVLGCPDPVVHEIAYQYGKNVG
  IAFQLIDDVLDFTSCSDQMGKPTSADLKLGLATGPVLFACQQFPEMNAMIMRRFSLPGDV
  DRARQYVLQSDGVQQTTYLAQQYCHEAIREISKLRPSPERDALIQLSEIVLTRDK

• Sequence length: 415

Pathways

KEGG:

Terpenoid backbone biosynthesis

Reactome:

Ubiquinol biosynthesis

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Deafness-encephaloneuropathy-obesity-valvulopathy syndrome	Pathogenic; Likely pathogenic	rs1425736863, rs2132231934, rs119463988, rs1232289653, rs767499454, rs2491583718, rs1278404579, rs1835152848, rs1057519354	RCV001335650 RCV005033560 RCV000003393 RCV004786723 RCV003221752 RCV003221754 RCV003221755 RCV003225706 RCV000416401	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Cervical cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Coenzyme Q10 deficiency	Conflicting classifications of pathogenicity; Benign; Likely benign; Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
COENZYME Q10 DEFICIENCY, PRIMARY, 2	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOR VISION DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, ENCEPHALONEUROPATHY, OBESITY, VALVULOPATHY SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MITOCHONDRIAL DISEASE	—	ClinGen, GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OVARIAN SEROUS CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PDSS1-related disorder	Benign; Conflicting classifications of pathogenicity; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RETINITIS PIGMENTOSA 1	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Amyotrophic Lateral Sclerosis	Amyotrophic Lateral Sclerosis	BEFREE	31702471		★☆☆☆☆ Found in Text Mining only
Anxiety	Anxiety Disorder	BEFREE	30252721, 30878321, 31675602		★☆☆☆☆ Found in Text Mining only
Anxiety Disorders	Anxiety Disorder	BEFREE	30252721, 30878321, 31675602		★☆☆☆☆ Found in Text Mining only
Aortic Valve Insufficiency	Aortic Valve Insufficiency	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	32887635	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	30287033		★☆☆☆☆ Found in Text Mining only
Cerebellar Diseases	Cerebellar diseases	Pubtator	19096106	Associate	★☆☆☆☆ Found in Text Mining only
COENZYME Q10 DEFICIENCY	Coenzyme Q10 Deficiency	BEFREE	17332895		★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Coenzyme Q10 Deficiency	Coenzyme q10 deficiency	Pubtator	17332895	Associate	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Coenzyme Q10 Deficiency	Coenzyme q10 deficiency	Pubtator	19096106	Stimulate	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
COENZYME Q10 DEFICIENCY, PRIMARY, 2	Coenzyme Q10 Deficiency	CLINVAR_DG	17332895, 22494076		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COENZYME Q10 DEFICIENCY, PRIMARY, 2	Coenzyme Q10 Deficiency	UNIPROT_DG	17332895		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COENZYME Q10 DEFICIENCY, PRIMARY, 2	Coenzyme Q10 Deficiency	ORPHANET_DG	17332895		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COENZYME Q10 DEFICIENCY, PRIMARY, 2	Coenzyme Q10 Deficiency	GENOMICS_ENGLAND_DG	17332895, 22494076, 27604308		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COENZYME Q10 DEFICIENCY, PRIMARY, 2	Coenzyme Q10 Deficiency	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal Carcinoma	Colorectal Cancer	BEFREE	30521889, 31096110		★☆☆☆☆ Found in Text Mining only
Congenital heart disease	Congenital Heart Disease	BEFREE	28035386		★☆☆☆☆ Found in Text Mining only
Coronary heart disease	Coronary Heart Disease	BEFREE	28035386		★☆☆☆☆ Found in Text Mining only
Cutis marmorata	Cutis marmorata	HPO_DG			★☆☆☆☆ Found in Text Mining only
Deafness-encephaloneuropathy-obesity-valvulopathy syndrome	Deafness-Encephaloneuropathy-Obesity-Valvulopathy Syndrome	Orphanet			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Depressive disorder	Mental Depression	BEFREE	30252721		★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Type 2	Diabetes mellitus, type 2	Pubtator	21423737	Associate	★☆☆☆☆ Found in Text Mining only
Essential Tremor	Tremor	BEFREE	28948077		★☆☆☆☆ Found in Text Mining only
Eye Diseases	Eye disease	Pubtator	36420660	Associate	★☆☆☆☆ Found in Text Mining only
Hearing Loss Sensorineural	Hearing loss	Pubtator	33285023	Associate	★☆☆☆☆ Found in Text Mining only
Hyperlipidemia	Hyperlipidemia	BEFREE	31582800		★☆☆☆☆ Found in Text Mining only
Hyperparathyroidism	Hyperparathyroidism	BEFREE	28421299		★☆☆☆☆ Found in Text Mining only
Hyperphenylalaninaemia	Hyperphenylalaninemia	BEFREE	16135092		★☆☆☆☆ Found in Text Mining only
Hypoxia	Hypoxia	Pubtator	32887635	Associate	★☆☆☆☆ Found in Text Mining only
Idiopathic pulmonary arterial hypertension	Pulmonary arterial hypertension	HPO_DG			★☆☆☆☆ Found in Text Mining only
Immunologic Deficiency Syndromes	Immunologic Deficiency Syndromes	BEFREE	19193835		★☆☆☆☆ Found in Text Mining only
Macrocephaly	Macrocephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	30287033		★☆☆☆☆ Found in Text Mining only
Melanoma Cutaneous Malignant	Melanoma	Pubtator	32232919	Associate	★☆☆☆☆ Found in Text Mining only
Mental Depression	Mental Depression	BEFREE	30252721		★☆☆☆☆ Found in Text Mining only
Mild Mental Retardation	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mitochondrial Diseases	Mitochondrial disease	Pubtator	17332895	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	30521889, 31096110		★☆☆☆☆ Found in Text Mining only
Nonorganic psychosis	Nonorganic Psychosis	BEFREE	21334180		★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	Pubtator	21423737	Associate	★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	HPO_DG			★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic atrophy	Pubtator	33285023	Associate	★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	BEFREE	28948077		★☆☆☆☆ Found in Text Mining only
Peripheral Nervous System Diseases	Nervous System Diseases	HPO_DG			★☆☆☆☆ Found in Text Mining only
Polydactyly	Polydactyly	BEFREE	28035386		★☆☆☆☆ Found in Text Mining only
POLYDACTYLY, PREAXIAL II (disorder)	Polydactyly	BEFREE	28035386		★☆☆☆☆ Found in Text Mining only
Post-Traumatic Stress Disorder	Stress Disorder	BEFREE	29596995, 30056129		★☆☆☆☆ Found in Text Mining only
Psychotic Disorders	Psychosis	BEFREE	21334180		★☆☆☆☆ Found in Text Mining only
Pulmonary arterial hypertension	Pulmonary arterial hypertension	HPO_DG			★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	21334180		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Skin-picking	Skin-picking	BEFREE	27885889		★☆☆☆☆ Found in Text Mining only
SMALL PATELLA SYNDROME	SMALL PATELLA SYNDROME	BEFREE	31336002, 31461372		★☆☆☆☆ Found in Text Mining only
Stiff-Person Syndrome	Stiff-Person Syndrome	BEFREE	31336002, 31461372		★☆☆☆☆ Found in Text Mining only