PTDSS1 Gene Curation

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

DEVELOPMENTAL DELAY.
1. PMID: 35224839 - associates LOF variants w/ developmental delay. 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
Inheritance	Autosomal dominant
Prevalence Possible sources Orphanet Medline Plus Genetics	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. (0.5 variant points x 3)+(2 de novo x 0.5) = 2.5 points. c.805C>T p.Pro269Ser in Patient 1 - confirmed de novo. 1 point. c.794T>C p.Leu265Pro in patient 5 same patient described and counted in PMID: 29341480 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	Source:
Clinical Validity Classification Classifications (pts) Definitive (12pts) Strong (12pts) Moderate (7-11pts) Limited (0.1-6pts) No genetic evidence Refuted Disputed	Source:
Molecular Mechanism Mechanisms Loss of function Gain of function Dominant negative Unknown Other	Loss of function / Gain of function / Dominant Negative PMID: 29341480 - caused by activating de novo variants (per text) Gene has moderate LOEUF score of 0.78. No high frequency SV deletions in gnomAD. PMID: 24241535 Patient fibroblasts showed higher incorporation of radiolabel into phosphatidylserine and phosphatidylserine-derived phosphatidylethanolamine compared to control cells, indicating increase in phosphatidylserine sythesis.
Penetrance options Complete (100%) High (≥80%) Moderate (<80% and >20%) Low (≤20%) (list source/PMID)	Source:
Age of Onset options Congenital Pediatric Adolescent Adulthood Late adulthood (list source/PMID)	Congenital
Severity Options Embryonic lethal - presence of a pathogenic variant or variants is not compatible with life. The penetrance must be complete. Severe - presence of a pathogenic variant or variant(s) results in significantly reduced fitness. The penetrance must be complete or high. Moderate - significant morbidity or mortality due to clinical features, but fitness may not be reduced, or penetrance is reduced. Mild - Presence of a variant or variant(s) is not associated with reduced fitness, no significant morbidity or mortality, and/or penetrance is low. None - presence of a variant results in no phenotype. An example is recessive disorders in which no phenotype is reported in carriers.	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 Examples - The @GENE@ is associated with @inheritance pattern@ @condition@, which is characterized by @clinical features@ (PMIDs). - Variable expression or severity: The severity and expressivity of the disorder is highly variable, even within families. - If multiple conditions associated with the gene: It has also been associated with @inheritance pattern@ @condition@, which is characterized by @clinical features@ (PMIDs). - Limited evidence gene: The PCNA gene has been reported in individuals with early onset autosomal recessive ataxia (PMID: 33426167, 24911150), however, evidence supporting this gene-dIsease relationship is limited
Case ID, Curator name, Date, Jira ticket link

PTDSS1 Gene Curation

Lenz-Majewski syndrome