PTDSS2

phosphatidylserine synthase 2

Basic information

Region (hg38): 11:448267-491399

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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in PTDSS2

This is a list of pathogenic ClinVar variants found in the PTDSS2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-450471-C-T		not specified	Uncertain significance (Jul 29, 2023)
11-450514-C-T		not specified	Uncertain significance (Dec 12, 2023)
11-450546-G-A		not specified	Uncertain significance (Jul 14, 2023)
11-450607-T-C		not specified	Uncertain significance (Dec 07, 2023)
11-473916-G-T		not specified	Uncertain significance (Mar 21, 2023)
11-479108-G-A		not specified	Uncertain significance (Aug 30, 2021)
11-479111-A-G		not specified	Uncertain significance (Sep 22, 2021)
11-487039-C-T		not specified	Uncertain significance (Dec 20, 2023)
11-487453-C-A		not specified	Likely benign (Jan 27, 2022)
11-488241-G-A		not specified	Uncertain significance (Sep 20, 2023)
11-488535-A-G		not specified	Uncertain significance (Jan 04, 2022)
11-489589-T-A		not specified	Uncertain significance (Oct 17, 2023)
11-489618-C-G		not specified	Uncertain significance (Dec 16, 2023)
11-489643-C-G		not specified	Uncertain significance (Jan 19, 2024)
11-489643-C-T		not specified	Uncertain significance (Feb 28, 2023)
11-489672-G-A		not specified	Uncertain significance (May 26, 2024)
11-489679-T-A		not specified	Uncertain significance (Apr 19, 2024)
11-489696-G-A		not specified	Uncertain significance (Apr 04, 2024)
11-489999-A-G		not specified	Uncertain significance (Jun 19, 2024)
11-490056-G-A		not specified	Uncertain significance (Jan 23, 2024)
11-490067-C-T		not specified	Uncertain significance (Mar 29, 2023)
11-490449-G-A		not specified	Uncertain significance (Nov 22, 2023)
11-490472-G-A		not specified	Uncertain significance (Mar 14, 2023)
11-490479-A-G		not specified	Uncertain significance (May 16, 2023)
11-490526-G-A		not specified	Uncertain significance (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTDSS2	protein_coding	protein_coding	ENST00000308020	12	43126

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000139	0.998	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.57	200	273	0.732	0.0000175	3161
Missense in Polyphen		65	107.37	0.60537		1157
Synonymous	-0.911	140	127	1.10	0.00000981	954
Loss of Function	2.75	13	29.0	0.449	0.00000161	285

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000239	0.000239
Ashkenazi Jewish	0.000205	0.000198
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000197	0.000193
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.00	0.00

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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