SMPD2

sphingomyelin phosphodiesterase 2

Basic information

Region (hg38): 6:109440724-109443919

Links

ENSG00000135587 ∙ NCBI:6610 ∙ OMIM:603498 ∙ HGNC:11121 ∙ Uniprot:O60906 ∙ 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 SMPD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMPD2 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				1	1	2
missense			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	2	1

Variants in SMPD2

This is a list of pathogenic ClinVar variants found in the SMPD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-109441144-G-A		not specified	Uncertain significance (Dec 21, 2022)
6-109441365-C-T		not specified	Uncertain significance (Apr 18, 2023)
6-109441381-C-G		not specified	Uncertain significance (Sep 17, 2021)
6-109441436-C-G		not specified	Uncertain significance (Nov 30, 2022)
6-109442017-A-G		not specified	Uncertain significance (Feb 23, 2023)
6-109442285-G-A		not specified	Uncertain significance (Jun 29, 2023)
6-109442774-G-A		not specified	Uncertain significance (Sep 21, 2023)
6-109442786-T-G		not specified	Uncertain significance (Sep 30, 2024)
6-109442830-G-C			Benign (Apr 07, 2018)
6-109442853-A-G		not specified	Likely benign (Dec 04, 2021)
6-109442864-C-G		not specified	Uncertain significance (Jul 25, 2024)
6-109442977-G-A		not specified	Uncertain significance (Apr 04, 2024)
6-109443020-T-C		not specified	Uncertain significance (Jun 21, 2023)
6-109443023-G-C		not specified	Uncertain significance (Oct 20, 2023)
6-109443325-C-T		not specified	Uncertain significance (Aug 15, 2023)
6-109443346-C-G		not specified	Uncertain significance (Jan 24, 2024)
6-109443360-C-A		not specified	Uncertain significance (May 25, 2022)
6-109443363-A-G		not specified	Uncertain significance (Feb 11, 2022)
6-109443394-C-A		not specified	Uncertain significance (May 26, 2022)
6-109443535-C-T		not specified	Uncertain significance (Dec 15, 2022)
6-109443552-A-C		not specified	Uncertain significance (May 14, 2024)
6-109443558-G-A		not specified	Uncertain significance (Sep 12, 2023)
6-109443579-G-C		not specified	Uncertain significance (Jan 23, 2023)
6-109443613-C-T		not specified	Uncertain significance (Apr 26, 2024)
6-109443683-C-T			Likely benign (Apr 07, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMPD2	protein_coding	protein_coding	ENST00000258052	10	3157

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.55e-18	0.00135	125610	0	138	125748	0.000549

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.143	230	236	0.974	0.0000122	2754
Missense in Polyphen		47	55.455	0.84754		652
Synonymous	-0.129	100	98.4	1.02	0.00000542	850
Loss of Function	-0.589	25	22.0	1.14	0.00000101	239

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00127	0.00127
Ashkenazi Jewish	0.00	0.00
East Asian	0.000707	0.000653
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000528	0.000528
Middle Eastern	0.000707	0.000653
South Asian	0.00101	0.00101
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Converts sphingomyelin to ceramide. Hydrolyze 1-acyl-2- lyso-sn-glycero-3-phosphocholine (lyso-PC) and 1-O-alkyl-2-lyso- sn-glycero-3-phosphocholine (lyso-platelet-activating factor). The physiological substrate seems to be Lyso-PAF.
• Pathway: Sphingolipid signaling pathway - Homo sapiens (human);Sphingolipid metabolism - Homo sapiens (human);TNF alpha Signaling Pathway;Signal Transduction of S1P Receptor;Signal Transduction;phospholipids as signalling intermediaries;Metabolism of lipids;sphingomyelin metabolism/ceramide salvage;Metabolism;Glycosphingolipid metabolism;TNFR1-mediated ceramide production;TNF signaling;Death Receptor Signalling;Ceramide signalling;p75 NTR receptor-mediated signalling;Glycosphingolipid metabolism;Sphingolipid metabolism;TNF receptor signaling pathway ;p75(NTR)-mediated signaling (Consensus)

Recessive Scores

• pRec: 0.293

Intolerance Scores

• loftool: 0.664
• rvis_EVS: -0.11
• rvis_percentile_EVS: 45.36

Haploinsufficiency Scores

• pHI: 0.0717
• hipred: N
• hipred_score: 0.170
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.795

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smpd2
• Phenotype: normal phenotype

Gene ontology

• Biological process: sphingomyelin metabolic process;response to mechanical stimulus;intracellular signal transduction;ceramide biosynthetic process;positive regulation of ceramide biosynthetic process
• Cellular component: plasma membrane;integral component of plasma membrane;caveola
• Molecular function: sphingomyelin phosphodiesterase activity;metal ion binding