SGPP2

sphingosine-1-phosphate phosphatase 2, the group of Sphingosine-1-phosphate phosphatases

Basic information

Region (hg38): 2:222424543-222562621

Links

ENSG00000163082 ∙ NCBI:130367 ∙ OMIM:612827 ∙ HGNC:19953 ∙ Uniprot:Q8IWX5 ∙ 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 SGPP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGPP2 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			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in SGPP2

This is a list of pathogenic ClinVar variants found in the SGPP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-222424622-G-A		not specified	Uncertain significance (Mar 16, 2022)
2-222424687-G-A		not specified	Uncertain significance (Jun 23, 2023)
2-222424704-C-A		not specified	Uncertain significance (Oct 01, 2024)
2-222424726-G-A		not specified	Uncertain significance (Oct 02, 2023)
2-222424732-C-T		not specified	Uncertain significance (May 24, 2023)
2-222424738-C-T		not specified	Uncertain significance (Jun 11, 2024)
2-222424766-A-G		not specified	Uncertain significance (Sep 13, 2023)
2-222474569-C-T		not specified	Uncertain significance (Aug 17, 2022)
2-222474586-G-A		not specified	Likely benign (Aug 26, 2024)
2-222474589-G-A		not specified	Uncertain significance (Apr 05, 2023)
2-222474632-C-T		not specified	Uncertain significance (May 17, 2023)
2-222474646-G-A		not specified	Uncertain significance (May 20, 2024)
2-222474659-C-T		not specified	Uncertain significance (Mar 07, 2024)
2-222474686-T-C		not specified	Uncertain significance (Mar 25, 2024)
2-222521791-G-A		not specified	Uncertain significance (Aug 19, 2024)
2-222521816-G-A		not specified	Uncertain significance (Nov 20, 2024)
2-222521833-G-A		not specified	Uncertain significance (Sep 26, 2024)
2-222521881-A-T		not specified	Uncertain significance (Mar 28, 2024)
2-222525001-A-G		not specified	Uncertain significance (Dec 05, 2024)
2-222525026-C-T		not specified	Uncertain significance (May 14, 2024)
2-222558362-G-A		not specified	Likely benign (Jul 09, 2024)
2-222558374-G-A		not specified	Uncertain significance (Jun 29, 2023)
2-222558396-A-T		not specified	Uncertain significance (Dec 13, 2023)
2-222558416-G-A		not specified	Uncertain significance (Jun 07, 2024)
2-222558519-G-A		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SGPP2	protein_coding	protein_coding	ENST00000321276	5	136432

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00282	0.945	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0735	193	196	0.985	0.0000110	2536
Missense in Polyphen		65	75.264	0.86363		829
Synonymous	-1.43	99	82.5	1.20	0.00000514	851
Loss of Function	1.70	6	12.5	0.482	5.30e-7	178

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000880	0.0000879
Middle Eastern	0.000435	0.000435
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has specific phosphohydrolase activity towards sphingoid base 1-phosphates. Has high phosphohydrolase activity against dihydrosphingosine-1-phosphate and sphingosine-1-phosphate (S1P) in vitro. May play a role in attenuating intracellular sphingosine 1-phosphate (S1P) signaling. May play a role in pro-inflammatory signaling. {ECO:0000269|PubMed:12411432, ECO:0000269|PubMed:17113265}.
• Pathway: Sphingolipid signaling pathway - Homo sapiens (human);Sphingolipid metabolism - Homo sapiens (human);Sphingolipid Metabolism;Gaucher Disease;Globoid Cell Leukodystrophy;Metachromatic Leukodystrophy (MLD);Fabry disease;Krabbe disease;Sphingolipid Metabolism;Metabolism of lipids;Metabolism;Sphingolipid de novo biosynthesis;Sphingolipid metabolism;sphingosine and sphingosine-1-phosphate metabolism (Consensus)

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.221
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.91

Haploinsufficiency Scores

• pHI: 0.175
• hipred: N
• hipred_score: 0.278
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.594

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sgpp2
• Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: sphingosine metabolic process;dephosphorylation;sphingolipid biosynthetic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane
• Molecular function: sphingosine-1-phosphate phosphatase activity;dihydrosphingosine-1-phosphate phosphatase activity