SMPDL3B

sphingomyelin phosphodiesterase acid like 3B

Basic information

Region (hg38): 1:27934999-27959157

Links

ENSG00000130768 ∙ NCBI:27293 ∙ OMIM:617737 ∙ HGNC:21416 ∙ Uniprot:Q92485 ∙ 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 SMPDL3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMPDL3B 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			30	4	1	35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	5	2

Variants in SMPDL3B

This is a list of pathogenic ClinVar variants found in the SMPDL3B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-27935196-G-A		not specified	Uncertain significance (Jan 31, 2024)
1-27935233-G-C		not specified	Uncertain significance (Jan 24, 2024)
1-27935235-G-T		not specified	Uncertain significance (Mar 20, 2023)
1-27945249-G-A		not specified	Likely benign (Mar 21, 2022)
1-27945270-G-A		not specified	Likely benign (Nov 23, 2021)
1-27945306-C-T		not specified	Uncertain significance (Dec 21, 2022)
1-27945381-A-G		not specified	Uncertain significance (Mar 16, 2022)
1-27949087-G-A		not specified	Likely benign (Sep 17, 2021)
1-27949087-G-C		not specified	Uncertain significance (Jul 14, 2021)
1-27949109-C-T		not specified	Uncertain significance (Oct 25, 2023)
1-27949120-A-T		not specified	Uncertain significance (May 15, 2024)
1-27953226-T-C		not specified	Uncertain significance (May 08, 2024)
1-27953281-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-27953302-T-G		not specified	Uncertain significance (Aug 09, 2021)
1-27953319-C-A		not specified	Uncertain significance (May 30, 2023)
1-27953340-A-G		not specified	Uncertain significance (Feb 06, 2023)
1-27954359-T-A		not specified	Uncertain significance (Apr 09, 2024)
1-27954417-C-T		not specified	Uncertain significance (Nov 17, 2022)
1-27954460-G-A			Benign (May 21, 2018)
1-27955709-C-T		not specified	Uncertain significance (May 11, 2022)
1-27955760-A-G		not specified	Uncertain significance (Nov 30, 2021)
1-27955760-A-T		not specified	Uncertain significance (Apr 26, 2024)
1-27955843-C-T		not specified	Uncertain significance (Sep 16, 2021)
1-27956012-G-C		not specified	Uncertain significance (Dec 06, 2022)
1-27956014-G-T		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMPDL3B	protein_coding	protein_coding	ENST00000373894	8	24165

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.41e-9	0.271	125664	0	84	125748	0.000334

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.690	251	284	0.885	0.0000170	2981
Missense in Polyphen		84	96.507	0.87041		1140
Synonymous	0.920	112	125	0.895	0.00000876	904
Loss of Function	0.681	15	18.1	0.827	9.43e-7	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000235	0.000235
Ashkenazi Jewish	0.00	0.00
East Asian	0.000762	0.000761
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000396	0.000396
Middle Eastern	0.000762	0.000761
South Asian	0.000392	0.000392
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lipid-modulating phosphodiesterase (PubMed:26095358). Active on the surface of macrophages and dendritic cells and strongly influences macrophage lipid composition and membrane fluidity. Acts as a negative regulator of Toll-like receptor signaling (By similarity). {ECO:0000250|UniProtKB:P58242, ECO:0000269|PubMed:26095358}.

Intolerance Scores

• rvis_EVS: -0.02
• rvis_percentile_EVS: 52.15

Haploinsufficiency Scores

• pHI: 0.254
• hipred: N
• hipred_score: 0.170
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.138

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smpdl3b
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype

Gene ontology

• Biological process: sphingomyelin catabolic process;inflammatory response;biological_process;negative regulation of toll-like receptor signaling pathway;innate immune response;membrane lipid catabolic process;negative regulation of inflammatory response
• Cellular component: extracellular space;plasma membrane;anchored component of membrane;extracellular exosome
• Molecular function: sphingomyelin phosphodiesterase activity;phosphoric diester hydrolase activity;hydrolase activity, acting on glycosyl bonds;metal ion binding