GeneBe

PTDSS2

phosphatidylserine synthase 2

Basic information

Region (hg38): 11:448268-491399

Links

ENSG00000174915 ∙ NCBI:81490 ∙ OMIM:612793 ∙ HGNC:15463 ∙ Uniprot:Q9BVG9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PTDSS2 gene.

  • not_specified (52 variants)
  • not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTDSS2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000030783.3. 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.

EffectPLPVUSLBBSum
synonymous
0
missense
51
clinvar
1
clinvar
 52
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 51 1 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PTDSS2protein_codingprotein_codingENST00000308020 1243126
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.00001390.9981257120361257480.000143
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.572002730.7320.00001753161
Missense in Polyphen65107.370.605371157
Synonymous-0.9111401271.100.00000981954
Loss of Function2.751329.00.4490.00000161285

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002390.000239
Ashkenazi Jewish0.0002050.000198
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.0001970.000193
Middle Eastern0.0001090.000109
South Asian0.0001310.000131
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Catalyzes a base-exchange reaction in which the polar head group of phosphatidylethanolamine (PE) or phosphatidylcholine (PC) is replaced by L-serine. PTDSS2 is specific for phosphatatidylethanolamine and does not act on phosphatidylcholine.;
Pathway
Glycerophospholipid metabolism - Homo sapiens (human);phosphatidylserine biosynthesis II;Phospholipid Biosynthesis;Kennedy pathway from Sphingolipids;Metabolism of lipids;Metabolism;Synthesis of PS;Glycerophospholipid biosynthesis;Phospholipid metabolism (Consensus)

Recessive Scores

pRec
0.103

Intolerance Scores

loftool
0.231
rvis_EVS
-0.2
rvis_percentile_EVS
38.98

Haploinsufficiency Scores

pHI
0.171
hipred
Y
hipred_score
0.639
ghis
0.511

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.563

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ptdss2
Phenotype
reproductive system 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); homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype;

Gene ontology

Biological process
phosphatidylserine biosynthetic process
Cellular component
endoplasmic reticulum membrane;membrane;integral component of membrane
Molecular function
CDP-diacylglycerol-serine O-phosphatidyltransferase activity;transferase activity