PDSS2

Chr 6AR

decaprenyl diphosphate synthase subunit 2

Also known as: C6orf210, COQ10D3, COQ1B, DLP1, bA59I9.3, hDLP1

NCBI Gene: 57107ENSG00000164494UniProt: Q86YH6OMIM: 610564

The protein encoded by this gene is an enzyme that synthesizes 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 isopentyl diphosphate in the assembly of polyisoprenoid side chains, the first step in coenzyme Q biosynthesis. Defects in this gene are a cause of coenzyme Q10 deficiency.[provided by RefSeq, Oct 2009]

GeneReviewsOMIMResearchGenerating clinical summary…
LOFmechanismARLOEUF 1.131 OMIM phenotype
Clinical Summary— PDSS2
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Gene-Disease Validity (ClinGen)
Leigh syndrome · ARModerate

Moderate evidence — consider for supplementary testing

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Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
6 unique Pathogenic / Likely Pathogenic· 132 VUS of 287 total submissions
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Clinical Trials
2 active or recruiting trials — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →
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GeneReview available — PDSS2
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?
1.13LOEUF
pLI 0.000
Z-score 1.12
OE 0.72 (0.48–1.13)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?
0.47Z-score
OE missense 0.91 (0.81–1.02)
196 obs / 215.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.72 (0.48–1.13)
0≤0.351.4
Missense OE?0.91 (0.81–1.02)
0≤0.61.4
Synonymous OE?0.89
0≤1.21.6
LoF obs/exp: 14 / 19.3Missense obs/exp: 196 / 215.6Syn Z: 0.81
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitivePDSS2-related coenzyme Q10 deficiency, primaryLOFAR

This gene — mechanism propensity

Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.

DN
0.6842th %ile
GOF
0.4777th %ile
LOF
0.3940th %ile

The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

287 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic2
Likely Pathogenic4
VUS132
Likely Benign117
Benign17
Conflicting11
2
Pathogenic
4
Likely Pathogenic
132
VUS
117
Likely Benign
17
Benign
11
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
2
0
0
0
2
Likely Pathogenic
3
1
0
0
4
VUS
5
115
10
2
132
Likely Benign
0
2
48
67
117
Benign
0
2
15
0
17
Conflicting
—11
Total101207369283

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

20 pathogenic / likely-pathogenic (of 29) ClinVar copy-number / structural variants overlap PDSS2 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →

Protein Context — Lollipop Plot

PDSS2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients