PDSS1

decaprenyl diphosphate synthase subunit 1

Basic information

Region (hg38): 10:26697700-26746798

Previous symbols: [ "TPRT" ]

Links

ENSG00000148459 ∙ NCBI:23590 ∙ OMIM:607429 ∙ HGNC:17759 ∙ Uniprot:Q5T2R2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• deafness-encephaloneuropathy-obesity-valvulopathy syndrome (Strong), mode of inheritance: AR
• deafness-encephaloneuropathy-obesity-valvulopathy syndrome (Moderate), mode of inheritance: AR
• deafness-encephaloneuropathy-obesity-valvulopathy syndrome (Supportive), mode of inheritance: AR
• deafness-encephaloneuropathy-obesity-valvulopathy syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Coenzyme Q10 deficiency 2	AR	Biochemical	There can be a wide range of manifestations, and in some individuals, treatment with Coenzyme Q10 supplementation can be beneficial	Audiologic/Otolaryngologic; Biochemical; Cardiovascular; Endocrine; Gastrointestinal; Hematologic; Musculoskeletal; Neurologic; Renal	17332895; 22231380

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDSS1 gene.

• not provided (242 variants)
• Deafness-encephaloneuropathy-obesity-valvulopathy syndrome (61 variants)
• not specified (23 variants)
• Inborn genetic diseases (13 variants)
• Coenzyme Q10 deficiency (3 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDSS1 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				44		44
missense			83	2	2	87
nonsense		1	4			5
start loss						0
frameshift	2	1	4			7
inframe indel			3			3
splice donor/acceptor (+/-2bp)						0
splice region		1	10	9	1	21
non coding			7	31	49	87
Total	2	2	101	77	51

Highest pathogenic variant AF is 0.0000132

Variants in PDSS1

This is a list of pathogenic ClinVar variants found in the PDSS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-26697729-G-A			Likely pathogenic (Jan 03, 2023)
10-26697745-T-C			Uncertain significance (Sep 13, 2022)
10-26697745-T-G		Inborn genetic diseases	Uncertain significance (Sep 14, 2022)
10-26697746-G-A		Inborn genetic diseases	Uncertain significance (Oct 06, 2022)
10-26697752-G-C			Uncertain significance (Apr 23, 2022)
10-26697753-G-C			Uncertain significance (Jun 02, 2021)
10-26697758-C-T			Uncertain significance (Mar 24, 2022)
10-26697762-G-A		Deafness-encephaloneuropathy-obesity-valvulopathy syndrome	Conflicting classifications of pathogenicity (Jul 17, 2023)
10-26697764-C-G			Uncertain significance (Jun 27, 2022)
10-26697767-G-A		Inborn genetic diseases	Uncertain significance (Oct 26, 2021)
10-26697771-C-T			Likely benign (Sep 11, 2023)
10-26697780-C-G			Likely benign (Jan 01, 2023)
10-26697780-C-T			Likely benign (Jun 03, 2023)
10-26697781-G-C		Deafness-encephaloneuropathy-obesity-valvulopathy syndrome • Inborn genetic diseases	Uncertain significance (Jul 19, 2022)
10-26697785-C-T		not specified	Conflicting classifications of pathogenicity (Nov 01, 2022)
10-26697788-C-T			Uncertain significance (Nov 01, 2021)
10-26697789-C-A			Likely benign (Nov 07, 2023)
10-26697789-C-G			Likely benign (Feb 20, 2022)
10-26697793-CG-GC			Uncertain significance (May 27, 2022)
10-26697794-G-A			Uncertain significance (Aug 10, 2023)
10-26697794-G-T		Deafness-encephaloneuropathy-obesity-valvulopathy syndrome	Uncertain significance (May 24, 2022)
10-26697800-G-C			Uncertain significance (Mar 18, 2022)
10-26697800-G-T		not specified • Deafness-encephaloneuropathy-obesity-valvulopathy syndrome	Benign (Jan 30, 2024)
10-26697805-T-A		Deafness-encephaloneuropathy-obesity-valvulopathy syndrome	Uncertain significance (Aug 30, 2018)
10-26697805-T-G		Inborn genetic diseases	Uncertain significance (Apr 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDSS1	protein_coding	protein_coding	ENST00000376215	12	49140

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.24e-8	0.929	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.32	161	215	0.747	0.0000124	2674
Missense in Polyphen		50	82.51	0.60598		1024
Synonymous	0.766	69	77.6	0.889	0.00000476	809
Loss of Function	1.85	16	26.2	0.611	0.00000177	285

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000351	0.000351
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000211	0.000211
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

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, 2 (COQ10D2) [MIM:614651]: An autosomal recessive multisystem disorder characterized by early-onset deafness, optic atrophy, mild mental retardation, peripheral neuropathy, obesity, livedo reticularis, and cardiac valvulopathy. {ECO:0000269|PubMed:17332895}. 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: 0.290

Intolerance Scores

• loftool: 0.385
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• pHI: 0.513
• hipred: Y
• hipred_score: 0.527
• ghis: 0.576

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.136

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pdss1

Gene ontology

• Biological process: ubiquinone biosynthetic process;isoprenoid biosynthetic process;protein heterotetramerization
• Cellular component: mitochondrial matrix;transferase complex
• Molecular function: trans-hexaprenyltranstransferase activity;metal ion binding;protein heterodimerization activity;trans-octaprenyltranstransferase activity