PTDSS1
Basic information
Region (hg38): 8:96261902-96336995
Links
Phenotypes
GenCC
Source:
- Lenz-Majewski hyperostotic dwarfism (Definitive), mode of inheritance: AD
- Lenz-Majewski hyperostotic dwarfism (Strong), mode of inheritance: AD
- Lenz-Majewski hyperostotic dwarfism (Strong), mode of inheritance: AD
- Lenz-Majewski hyperostotic dwarfism (Supportive), mode of inheritance: AD
- Lenz-Majewski hyperostotic dwarfism (Limited), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Lenz-Majewski hyperostotic dwarfism | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Dental; Genitourinary; Musculoskeletal; Neurologic | 24241535 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (178 variants)
- Inborn_genetic_diseases (40 variants)
- Lenz-Majewski_hyperostosis_syndrome (14 variants)
- PTDSS1-related_disorder (8 variants)
- not_specified (2 variants)
- Microcephaly (1 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTDSS1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014754.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 39 | 45 | ||||
missense | 82 | 17 | 111 | |||
nonsense | 5 | |||||
start loss | 0 | |||||
frameshift | 4 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
Total | 4 | 3 | 92 | 57 | 10 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PTDSS1 | protein_coding | protein_coding | ENST00000517309 | 13 | 75281 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.151 | 0.849 | 125730 | 0 | 18 | 125748 | 0.0000716 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 2.38 | 158 | 267 | 0.591 | 0.0000137 | 3159 |
Missense in Polyphen | 45 | 103.12 | 0.43637 | 1266 | ||
Synonymous | 0.470 | 92 | 97.9 | 0.940 | 0.00000553 | 857 |
Loss of Function | 3.95 | 8 | 32.2 | 0.248 | 0.00000166 | 313 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000218 | 0.000210 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000109 | 0.000109 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.0000712 | 0.0000703 |
Middle Eastern | 0.000109 | 0.000109 |
South Asian | 0.00 | 0.00 |
Other | 0.000326 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Catalyzes a base-exchange reaction in which the polar head group of phosphatidylethanolamine (PE) or phosphatidylcholine (PC) is replaced by L-serine. In membranes, PTDSS1 catalyzes mainly the conversion of phosphatidylcholine. Also converts, in vitro and to a lesser extent, phosphatidylethanolamine.;
- Disease
- DISEASE: Lenz-Majewski hyperostotic dwarfism (LMHD) [MIM:151050]: A syndrome of intellectual disability and multiple congenital anomalies that features generalized craniotubular hyperostosis. LMHD is characterized by the combination of sclerosing bone dysplasia, intellectual disability and distinct craniofacial, dental, cutaneous and distal limb anomalies. The progressive generalized hyperostosis associated with this syndrome affects the cranium, the vertebrae and the diaphyses of tubular bones, leading to severe growth restriction. {ECO:0000269|PubMed:24241535}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Glycerophospholipid metabolism - Homo sapiens (human);Phospholipid Biosynthesis;Kennedy pathway from Sphingolipids;Metabolism of lipids;Metabolism;phosphatidylserine biosynthesis I;Synthesis of PS;Glycerophospholipid biosynthesis;Phospholipid metabolism
(Consensus)
Recessive Scores
- pRec
- 0.128
Intolerance Scores
- loftool
- 0.516
- rvis_EVS
- -0.36
- rvis_percentile_EVS
- 28.93
Haploinsufficiency Scores
- pHI
- 0.269
- hipred
- Y
- hipred_score
- 0.685
- ghis
- 0.560
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.938
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ptdss1
- Phenotype
- homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);
Gene ontology
- Biological process
- phosphatidylserine biosynthetic process
- Cellular component
- endoplasmic reticulum membrane;membrane;integral component of membrane
- Molecular function
- transferase activity