PDSS2

decaprenyl diphosphate synthase subunit 2

Basic information

Region (hg38): 6:107152561-107459564

Previous symbols: [ "C6orf210" ]

Links

ENSG00000164494 ∙ NCBI:57107 ∙ OMIM:610564 ∙ HGNC:23041 ∙ Uniprot:Q86YH6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• coenzyme Q10 deficiency, primary, 3 (Definitive), mode of inheritance: AR
• Leigh syndrome with nephrotic syndrome (Supportive), mode of inheritance: AR
• coenzyme Q10 deficiency, primary, 3 (Strong), mode of inheritance: AR
• Leigh syndrome (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Coenzyme Q10 deficiency 3	AR	Biochemical	Treatment with Coenzyme Q10 supplementation may be beneficial	Biochemical; Neurologic; Renal	17186472; 22231380

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDSS2 gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDSS2 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				52		52
missense		2	74	3	2	81
nonsense			4			4
start loss			1			1
frameshift			1			1
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1					1
splice region			3	6		9
non coding			3	36	14	53
Total	1	2	84	91	16

Variants in PDSS2

This is a list of pathogenic ClinVar variants found in the PDSS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-107152586-C-CT		Coenzyme Q10 deficiency	Uncertain significance (Jun 14, 2016)
6-107152732-G-GTT		Coenzyme Q10 deficiency	Uncertain significance (Jun 14, 2016)
6-107153850-C-T		Coenzyme Q10 deficiency	Uncertain significance (Jun 14, 2016)
6-107154074-T-TA		Coenzyme Q10 deficiency	Likely benign (Jun 14, 2016)
6-107154308-C-T			Benign (Jun 26, 2018)
6-107154618-G-A		not specified	Likely benign (May 04, 2016)
6-107154625-A-C			Uncertain significance (Sep 01, 2022)
6-107154627-ATC-A		Coenzyme Q10 deficiency, primary, 3	Uncertain significance (Apr 02, 2022)
6-107154665-C-G			Uncertain significance (Nov 19, 2023)
6-107154668-G-T		Coenzyme Q10 deficiency, primary, 3	Uncertain significance (Jan 21, 2020)
6-107154670-C-T		not specified	Benign/Likely benign (Oct 03, 2023)
6-107154673-C-T		Focal segmental glomerulosclerosis	Conflicting classifications of pathogenicity (Jan 30, 2024)
6-107154674-G-A		Coenzyme Q10 deficiency, primary, 3 • Nephrotic syndrome • not specified	Conflicting classifications of pathogenicity (Dec 30, 2022)
6-107154679-A-T			Likely benign (May 17, 2022)
6-107154685-G-A		not specified • Coenzyme Q10 deficiency, primary, 3	Benign/Likely benign (Nov 18, 2023)
6-107154692-A-G			Uncertain significance (Aug 16, 2022)
6-107154694-G-C			Likely benign (Oct 24, 2022)
6-107154696-C-T			Uncertain significance (Aug 21, 2022)
6-107154703-T-G			Likely benign (Oct 13, 2023)
6-107154710-T-C			Uncertain significance (Jul 23, 2022)
6-107154722-C-T		Inborn genetic diseases	Uncertain significance (May 05, 2023)
6-107154723-G-A		Coenzyme Q10 deficiency, primary, 3 • Inborn genetic diseases	Uncertain significance (Sep 14, 2022)
6-107154745-C-T			Likely benign (Jan 17, 2023)
6-107154749-C-A		Coenzyme Q10 deficiency, primary, 3	Uncertain significance (Nov 16, 2020)
6-107154773-C-T		not specified • Coenzyme Q10 deficiency, primary, 3 • Inborn genetic diseases • PDSS2-related disorder	Conflicting classifications of pathogenicity (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDSS2	protein_coding	protein_coding	ENST00000369037	8	307008

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.37e-8	0.604	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.474	196	216	0.909	0.0000100	2603
Missense in Polyphen		50	72.473	0.68992		871
Synonymous	0.813	74	83.4	0.887	0.00000400	789
Loss of Function	1.12	14	19.3	0.724	8.59e-7	234

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00149	0.00149
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000163	0.000163
South Asian	0.000131	0.000131
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Supplies decaprenyl diphosphate, the precursor for the side chain of the isoprenoid quinones ubiquinone-10. {ECO:0000269|PubMed:16262699}.
• Disease: DISEASE: Coenzyme Q10 deficiency, primary, 3 (COQ10D3) [MIM:614652]: A fatal encephalomyopathic form of coenzyme Q10 deficiency with nephrotic syndrome. Coenzyme Q10 deficiency is an autosomal recessive disorder with variable manifestations consistent with 5 major phenotypes. The phenotypes include an encephalomyopathic form with seizures and ataxia; a multisystem infantile form with encephalopathy, cardiomyopathy and renal failure; a predominantly cerebellar form with ataxia and cerebellar atrophy; Leigh syndrome with growth retardation; and an isolated myopathic form. {ECO:0000269|PubMed:17186472}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Terpenoid backbone biosynthesis - Homo sapiens (human);Metabolism;Ubiquinol biosynthesis;Metabolism of cofactors;Metabolism of vitamins and cofactors;ubiquinol-10 biosynthesis (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.742
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.54

Haploinsufficiency Scores

• pHI: 0.0767
• hipred: N
• hipred_score: 0.303
• ghis: 0.519

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0635

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pdss2
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; muscle phenotype; growth/size/body region phenotype; renal/urinary system phenotype; skeleton phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary 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); respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: ubiquinone biosynthetic process;isoprenoid biosynthetic process;regulation of body fluid levels;protein heterotetramerization
• Cellular component: mitochondrial matrix;cytosol;transferase complex
• Molecular function: trans-hexaprenyltranstransferase activity;protein heterodimerization activity;trans-octaprenyltranstransferase activity