SMPDL3A

sphingomyelin phosphodiesterase acid like 3A

Basic information

Region (hg38): 6:122789049-122809720

Links

ENSG00000172594 ∙ NCBI:10924 ∙ OMIM:610728 ∙ HGNC:17389 ∙ Uniprot:Q92484 ∙ 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 SMPDL3A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SMPDL3A 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 SMPDL3A

This is a list of pathogenic ClinVar variants found in the SMPDL3A region.

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

Position	Type	Phenotype	Significance	ClinVar
6-122789356-G-A		not specified	Uncertain significance (Sep 11, 2024)
6-122789365-C-T		not specified	Uncertain significance (Jul 17, 2024)
6-122789368-G-C		not specified	Uncertain significance (Jan 22, 2024)
6-122789377-C-G		not specified	Uncertain significance (Apr 27, 2022)
6-122789417-C-T		not specified	Uncertain significance (Aug 12, 2021)
6-122795716-C-T		not specified	Uncertain significance (Dec 15, 2023)
6-122795780-C-A		not specified	Uncertain significance (Jun 10, 2022)
6-122795872-C-T		not specified	Uncertain significance (Jul 15, 2021)
6-122795879-G-T		not specified	Uncertain significance (Feb 23, 2023)
6-122796917-T-G		not specified	Uncertain significance (Feb 17, 2024)
6-122796940-C-T		not specified	Uncertain significance (Mar 11, 2022)
6-122801331-A-G		not specified	Uncertain significance (Oct 06, 2022)
6-122801376-G-A		not specified	Uncertain significance (Oct 20, 2024)
6-122801388-A-G		not specified	Uncertain significance (Mar 29, 2022)
6-122803697-C-G		not specified	Uncertain significance (Feb 05, 2024)
6-122803795-G-C		not specified	Uncertain significance (Dec 07, 2021)
6-122804919-T-C		not specified	Uncertain significance (Feb 27, 2023)
6-122804937-G-T		not specified	Uncertain significance (Jul 14, 2023)
6-122805018-G-A		not specified	Uncertain significance (Apr 01, 2024)
6-122805021-A-T		not specified	Uncertain significance (Dec 19, 2023)
6-122805065-A-G		not specified	Uncertain significance (Jul 22, 2024)
6-122806328-C-G		not specified	Uncertain significance (Oct 05, 2023)
6-122809101-A-G		not specified	Uncertain significance (Sep 10, 2024)
6-122809188-A-C		not specified	Uncertain significance (Apr 12, 2024)
6-122809400-A-T		not specified	Uncertain significance (Jul 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SMPDL3A	protein_coding	protein_coding	ENST00000368440	8	20551

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.28e-21	0.000120	125489	0	259	125748	0.00103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.155	225	232	0.971	0.0000104	2986
Missense in Polyphen		89	98.316	0.90525		1242
Synonymous	0.607	80	87.2	0.917	0.00000417	836
Loss of Function	-1.36	27	20.4	1.33	8.60e-7	254

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00157	0.00157
Ashkenazi Jewish	0.00	0.00
East Asian	0.00756	0.00759
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000486	0.000484
Middle Eastern	0.00756	0.00759
South Asian	0.000362	0.000359
Other	0.00116	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has in vitro nucleotide phosphodiesterase activity with nucleoside triphosphates, such as ATP (PubMed:25288789, PubMed:26783088). Has in vitro activity with p-nitrophenyl-TMP (PubMed:25288789). Has lower activity with nucleoside diphosphates, and no activity with nucleoside monophosphates (PubMed:25288789, PubMed:26783088). Has in vitro activity with CDP-choline, giving rise to CMP and phosphocholine. Has in vitro activity with CDP-ethanolamine (PubMed:26783088). Does not have sphingomyelin phosphodiesterase activity (PubMed:25288789, PubMed:26783088). {ECO:0000269|PubMed:25288789, ECO:0000269|PubMed:26783088}.

Recessive Scores

• pRec: 0.126

Intolerance Scores

• loftool: 0.351
• rvis_EVS: 0.57
• rvis_percentile_EVS: 82.08

Haploinsufficiency Scores

• pHI: 0.0541
• hipred: N
• hipred_score: 0.251
• ghis: 0.388

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000369

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Smpdl3a

Gene ontology

• Biological process: sphingomyelin catabolic process;nucleoside triphosphate catabolic process
• Cellular component: extracellular space;extracellular exosome
• Molecular function: sphingomyelin phosphodiesterase activity;protein binding;phosphoric diester hydrolase activity;zinc ion binding