SGMS1

sphingomyelin synthase 1, the group of Sterile alpha motif domain containing

Basic information

Region (hg38): 10:50305585-50625163

Previous symbols: [ "TMEM23" ]

Links

ENSG00000198964 ∙ NCBI:259230 ∙ OMIM:611573 ∙ HGNC:29799 ∙ Uniprot:Q86VZ5 ∙ 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 SGMS1 gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGMS1 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in SGMS1

This is a list of pathogenic ClinVar variants found in the SGMS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-50308098-C-T		not specified	Uncertain significance (Aug 10, 2021)
10-50308139-C-T		not specified	Uncertain significance (Aug 17, 2022)
10-50311331-T-A		not specified	Uncertain significance (May 31, 2023)
10-50343654-G-A		not specified	Uncertain significance (Sep 26, 2023)
10-50343735-T-G		not specified	Uncertain significance (Nov 17, 2022)
10-50343804-G-C		not specified	Uncertain significance (Sep 17, 2021)
10-50343850-C-A		not specified	Uncertain significance (Nov 13, 2023)
10-50343928-T-G		not specified	Uncertain significance (Feb 02, 2024)
10-50343963-C-T		not specified	Uncertain significance (Feb 05, 2024)
10-50344054-T-C		not specified	Uncertain significance (Dec 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SGMS1	protein_coding	protein_coding	ENST00000361781	5	319564

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.945	0.0549	125740	0	5	125745	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.67	125	242	0.517	0.0000133	2728
Missense in Polyphen		35	89.864	0.38948		967
Synonymous	-0.0734	93	92.1	1.01	0.00000549	785
Loss of Function	3.80	3	22.4	0.134	0.00000138	216

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Sphingomyelin synthases synthesize the sphingolipid, sphingomyelin, through transfer of the phosphatidyl head group, phosphatidylcholine, on to the primary hydroxyl of ceramide. The reaction is bidirectional depending on the respective levels of the sphingolipid and ceramide. Golgi apparatus SMS1 directly and specifically recognizes the choline head group on the substrate, requiring two fatty chains on the choline-P donor molecule in order to be recognized efficiently as a substrate. Major form in macrophages. Required for cell growth in certain cell types such as HeLa cells. Suppresses BAX-mediated apoptosis and also prevents cell death in response to stimuli such as hydrogen peroxide, osmotic stress, elevated temperature and exogenously supplied sphingolipids. May protect against cell death by reversing the stress-inducible increase in levels of proapoptotic ceramide. {ECO:0000269|PubMed:14685263, ECO:0000269|PubMed:17449912}.
• 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;Metabolism of lipids;sphingomyelin metabolism/ceramide salvage;Metabolism;Glycosphingolipid metabolism;Sphingolipid de novo biosynthesis;Sphingolipid metabolism;IL2 signaling events mediated by PI3K (Consensus)

Recessive Scores

• pRec: 0.388

Intolerance Scores

• loftool: 0.436
• rvis_EVS: -0.45
• rvis_percentile_EVS: 24

Haploinsufficiency Scores

• pHI: 0.284
• hipred: Y
• hipred_score: 0.728
• ghis: 0.656

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.659

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sgms1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; hematopoietic 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); reproductive system phenotype; skeleton phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: sphingomyelin biosynthetic process;apoptotic process;inflammatory response;positive regulation of gene expression;phosphorylation;sphingolipid biosynthetic process;ceramide biosynthetic process;cellular response to lipopolysaccharide;cellular response to tumor necrosis factor;regulation of intrinsic apoptotic signaling pathway
• Cellular component: Golgi trans cisterna;Golgi membrane;nucleus;endoplasmic reticulum;plasma membrane;integral component of plasma membrane;membrane;integral component of Golgi membrane;integral component of endoplasmic reticulum membrane
• Molecular function: ceramide phosphoethanolamine synthase activity;kinase activity;sphingomyelin synthase activity;ceramide cholinephosphotransferase activity