PTDSS1 Gene Curation

1 Lenz-Majewski syndrome

Gene-disease assertions not curated here (add link or write note):

DEVELOPMENTAL DELAY.
1. PMID: 35224839 - asserts that LOF variants are associated w developmental delay, but only describe missense variant. Describes p.Leu137Phe missense variant in 1 child, de novo, with mild to moderate developmental delay. Overexpressed variant in HEK293 cells, observed variant displayed no catalytic activity. Gene is not missense constrained, has a moderate LOEUF score of 0.78. At most 1.1 point (adding functional 0.5, de novo 0.5, missense common disease 0.1 points). Another variant c.421A>G (p.Thr141Ala) de novo in patient with possible developmental delay. Not scoring this because the phenotype is vague/unclear.
2. PubMed: 33057194 - c.284G>A p.R95Q de novo in patient 20399, but multiple de novo variants found, see supplemental table 1
3. PMID: 35982159 0 supplemental data 3; same patient as 33057194
Agenesis of corpus callosum and ventriculomegaly (fetal imaging) -
1. PMID: 36307859 and 36307859 (overlapping authors, likely same fetus). In Supplement, classified as VUS, described as de novo. Agenesis of the corpous callosum is a feature of Lenz-Majewsky dwarfism (PMID 29341480)
2. Deletion hg19 arr8q22.1(97 214 184–98 480 468) × 1 in fetus with Macrocephaly, mild VM, dysplastic CC, signs of MCD, overgrowth. Deletion impacts at least 7 other genes.

Disease	Lenz-Majewski syndrome

Disease	Lenz-Majewski syndrome
Inheritance	Autosomal dominant
Prevalence Orphanet Medline Plus Genetics	VERY RARE Source:
Rapid or full curation?	Rapid Full
ClinGen / GenCC / BabySeq / HGMD / OMIM	No ClinGen curation. GenCC conflicting w/ US labs: Strong by Invitae, limited by Ambry. HGMD variants curated in Clinical Validity scoring. This is the only phenotype listed for this gene in OMIM.
Clinical Validity Scoring Notes and points	It appears the phenotype is so specific that several studies only sequenced this gene. Did not penalize the scoring for this reason. PMID: 24241535 author overlap with PMID 29341480 . See supplement table 1 c.1058A>G p.Q353R recurrent variant, identified in patients 2-4. Confirmed de novo in patient 3 and 4. Variant injected into zebrafish embryo and showed craniofacial abnormalities. (0.5 variant/patient points x 3)+(2 de novo x 0.5) +0.5 functional evidence = 3 points. c.805C>T p.Pro269Ser in Patient 1 - confirmed de novo. Variant injected into zebrafish embryo and showed craniofacial abnormalities. 1.5 point. c.794T>C p.Leu265Pro in patient 5 same patient described and counted in PMID: 29341480. Variant injected into zebrafish embryo and showed craniofacial abnormalities. 0.5 POINT PMID: 29341480 Sequencing of PTDSS1 only. NM_014754.3:c.794T>C (p. Leu265Pro) in patient 1 (exon 7). Same patient as patient previously reported in PMID:24241535 parents not available. REVEL Score: 0.877, absent gnomAD. NM_014754.3:c.284G>T(p.Arg95Leu) mutation in exon3 in patient 2 parents not available. REVEL Score: 0.778. Absent gnomAD 0.5 POINTS NM_014754.3:c.806C>T (p.Pro269Leu) in exon 7 in patient 3 de novo inheritance was confirmed. REVEL 0.819. Absent gnomAD - 1 POINT PMID: 31403251 NM_014754.3:c.284G>T(p.Arg95Leu) (reported in 9341480) in a patient with Lenz-Majewski syndrome. Reportedly de novo. Sequencing of PTDSS1 gene only. 1 POINT Source:
Clinical Validity Points Total	7.5
Clinical Validity Classification Definitive (12pts) Strong (12pts) Moderate (7-11pts) Limited (0.1-6pts) No genetic evidence Refuted Disputed	At least MODERATE. (I stopped curation at this point because the variant I am working on will only reach VUS as LOF is not a mechanism of disease) Source: 24241535, 29341480, 31403251.
Molecular Mechanism Loss of function Gain of function Dominant negative Unknown Other	Likely Gain of function Sources: 24241535, 27044099 Gene has moderate LOEUF score of 0.78. No high frequency SV deletions in gnomAD. PMID: 24241535 - supports GOF mechanism by functional evidence. Summary from abstract: “Phosphatidylserine synthesis was increased in intact fibroblasts from affected individuals, and end-product inhibition of PSS1 by phosphatidylserine was markedly reduced. Therefore, these mutations cause a gain-of-function effect associated with regulatory dysfunction of PSS1.” Patient fibroblasts showed higher incorporation of radiolabel into phosphatidylserine and phosphatidylserine-derived phosphatidylethanolamine compared to control cells, indicating increase in phosphatidylserine synthesis. Patient fibroblasts showed incorporation of 3H serine into phosphatidylserine and phosphatidylethanolamine that was resistant to inhibition by phosphatidylserine Therefore, patient mutations render the enzyme PSS1 resistant to feedback inhibition by phosphatidylserine. PMID: 27044099 HEK293 cells. Expression of mutant PSS1 enzymes showed a significant increase in PS synthesis and accumulates in the ER. They showed significantly reduced levels of PI4P both in the Golgi and the PM by activating the Sac1 phosphatase. Inhibitors of PI4KA blocked PS synthesis and reduced PS levels by 50% in normal cells, but mutant enzymes alleviated the PI4P dependence of PS synthesis.
Penetrance Complete (100%) High (≥80%) Moderate (<80% and >20%) Low (≤20%) (list source/PMID)	Source:
Age of Onset Congenital Pediatric Adolescent Adulthood Late adulthood (list source/PMID)	Congenital
Severity	Severe
Clinical Features	Cutis laxa Facial dysmorphism Severe growth retardation Hypoerostotic skeletal dysplasia Intellectual disability Sources: 9341480
HPO Terms https://hpo.jax.org/app/
Gene SOPs & Notes	LINK if SOP is a long document. Short notes if it is easy to digest. eg. Last known truncating variant
Curation Summary	The PTDSS1 gene is associated with autosomal dominant Lenz-Majewski syndrome, a rare disease that is characterized by craniofacial, dental, cutaneous, and limb anomalies. Intellectual disability is also a feature (PMID: 24241535, 29341480, 31403251). Pathogenic variants are typically found to be de novo missense variants, and the molecular mechanism is likely gain-of-function (PMID: 24241535, 27044099). Variants in this gene have also been reported in individuals with developmental delay and/or autism; however, evidence supporting this gene-disease association is limited (PMID: 35224839, 33057194).
Case ID, Curator name, Date, Jira ticket link	SDSM-VS, AO, 11/6/2024

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