Disease | Lenz-Majewski syndrome |
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Inheritance | Autosomal dominant |
Prevalence | VERY RARE Source: |
Rapid or full curation? | |
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) = 2+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 NM_014754.3:c.284G>T(p.Arg95Leu) mutation in exon3 in patient 2 NM_014754.3:c.806C>T (p.Pro269Leu) in exon 7 in patient 3
PMID: 31403251 Source: |
Clinical Validity Points Total | Source: 7.5 |
Clinical Validity Classification | Expand |
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| title | Classifications (pts) |
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| 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 | Expand |
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| Loss of function Gain of function Dominant negative Unknown Other |
| Loss of function / Likely Gain of function / Dominant Negative PMID: 29341480 - caused by activating de novo variants (per text)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 sythesisphosphatidylserine 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.
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Penetrance | Expand |
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| Complete (100%) High (≥80%) Moderate (<80% and >20%) Low (≤20%) |
(list source/PMID) | Source: |
Age of Onset | Expand |
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| Congenital Pediatric Adolescent Adulthood Late adulthood |
(list source/PMID) | Congenital |
Severity | Expand |
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| 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 | Expand |
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| - 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 |
| 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 |