PDSS2

Chr 6AR

decaprenyl diphosphate synthase subunit 2

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

The encoded enzyme catalyzes the condensation of farnesyl diphosphate and isopentenyl diphosphate to produce prenyl diphosphates that serve as precursors for the side chain of coenzyme Q10, which is essential for mitochondrial respiratory chain function. Mutations cause autosomal recessive primary coenzyme Q10 deficiency, which can present with cerebellar ataxia, seizures, and other neurological manifestations. The gene is highly tolerant to loss-of-function variants (pLI near zero), consistent with its recessive inheritance pattern.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 1.131 OMIM phenotype
Clinical SummaryPDSS2
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Gene-Disease Validity (ClinGen)
Leigh syndrome · ARModerate

Moderate evidence — consider for supplementary testing

Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
1.13LOEUF
pLI 0.000
Z-score 1.12
OE 0.72 (0.481.13)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.47Z-score
OE missense 0.91 (0.811.02)
196 obs / 215.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.72 (0.481.13)
00.351.4
Missense OE0.91 (0.811.02)
00.61.4
Synonymous OE0.89
01.21.6
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

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

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

PDSS2 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold
Clinical Literature
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