ALDH18A1

Chr 10ADAR

aldehyde dehydrogenase 18 family member A1

Also known as: ADCL3, ARCL3A, GSAS, P5CS, PYCS, SPG9, SPG9A, SPG9B

The encoded bifunctional enzyme converts glutamate to glutamate 5-semialdehyde, a critical step in the biosynthesis of proline, ornithine and arginine. Mutations cause cutis laxa (both autosomal dominant and recessive forms) and hereditary spastic paraplegia (types 9A and 9B), with associated features including hyperammonemia, cataracts, and connective tissue abnormalities. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.52) and exhibits both autosomal dominant and recessive inheritance patterns depending on the specific condition.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt
MultiplemechanismAD/ARLOEUF 0.524 OMIM phenotypes
Clinical SummaryALDH18A1
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Gene-Disease Validity (ClinGen)
P5CS deficiency · SDDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.33) despite low pLI — interpret in context.
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GeneReview available — ALDH18A1
Authoritative clinical overview · Recommended first read
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Moderate LoF intolerance
LoF Constraint
0.52LOEUF
pLI 0.001
Z-score 3.94
OE 0.33 (0.210.52)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
1.97Z-score
OE missense 0.74 (0.670.81)
325 obs / 441.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.33 (0.210.52)
00.351.4
Missense OE0.74 (0.670.81)
00.61.4
Synonymous OE0.95
01.21.6
LoF obs/exp: 13 / 39.8Missense obs/exp: 325 / 441.2Syn Z: 0.48
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
limitedALDH18A1-related spastic paraplegia (biallelic)OTHERAR
definitiveALDH18A1-related cutis laxaGOFAD
definitiveALDH18A1-related spastic paraplegia (monoallelic)DNAD
definitiveALDH18A1-related developmental disorder-joint hypermobility-skin laxity with or without metabolic abnormalitiesLOFAR
DN
0.7326th %ile
GOF
0.5759th %ile
LOF
0.3843th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median · 1 literature citation

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Literature Evidence

DNImaging in cutis laxa syndrome caused by a dominant negative ALDH18A1 mutation, with hypotheses for intracranial vascular tortuosity and wide perivascular spaces.PMID:28757335

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

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

ALDH18A1 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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