SPTLC3

serine palmitoyltransferase long chain base subunit 3

Basic information

Region (hg38): 20:13008971-13169103

Previous symbols: [ "C20orf38", "SPTLC2L" ]

Links

ENSG00000172296 ∙ NCBI:55304 ∙ OMIM:611120 ∙ HGNC:16253 ∙ Uniprot:Q9NUV7 ∙ 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 SPTLC3 gene.

• Inborn genetic diseases (22 variants)
• not provided (1 variants)
• Sensory neuropathy;Peripheral neuropathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPTLC3 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		1	23			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	23	0	0

Highest pathogenic variant AF is 0.0000131

Variants in SPTLC3

This is a list of pathogenic ClinVar variants found in the SPTLC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-13009368-T-A		not specified	Uncertain significance (May 06, 2022)
20-13009370-G-A			Uncertain significance (Mar 01, 2023)
20-13048957-C-G		not specified	Uncertain significance (Oct 10, 2023)
20-13048979-T-C		not specified	Uncertain significance (Apr 19, 2023)
20-13049098-T-G		not specified	Uncertain significance (Jul 25, 2023)
20-13072400-T-C		Sensory neuropathy;Peripheral neuropathy	Likely pathogenic (Aug 18, 2015)
20-13074367-C-G		not specified	Uncertain significance (Dec 06, 2022)
20-13074371-G-T		not specified	Uncertain significance (Feb 03, 2022)
20-13093535-G-T		not specified	Uncertain significance (Feb 17, 2022)
20-13093554-C-T		not specified	Uncertain significance (Feb 09, 2023)
20-13110171-C-T		not specified	Uncertain significance (Jan 29, 2024)
20-13110172-G-A		not specified	Uncertain significance (Jun 27, 2023)
20-13110198-C-G		not specified	Uncertain significance (Mar 31, 2023)
20-13117541-T-G		not specified	Uncertain significance (Mar 29, 2022)
20-13117603-G-A		not specified	Uncertain significance (Apr 13, 2023)
20-13117619-G-A		not specified	Uncertain significance (Mar 23, 2023)
20-13117628-C-T		not specified	Uncertain significance (Sep 29, 2023)
20-13117645-G-T		not specified	Uncertain significance (Jan 23, 2023)
20-13117647-C-A		not specified	Uncertain significance (Apr 18, 2023)
20-13117666-C-A		not specified	Uncertain significance (Dec 08, 2023)
20-13117676-C-T		not specified	Uncertain significance (Oct 25, 2023)
20-13126597-G-A		not specified	Uncertain significance (Dec 06, 2021)
20-13126655-C-T		not specified	Uncertain significance (Dec 03, 2021)
20-13160040-G-A		not specified	Uncertain significance (Nov 17, 2023)
20-13160049-G-A		not specified	Uncertain significance (Oct 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPTLC3	protein_coding	protein_coding	ENST00000399002	12	157785

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.23e-7	0.985	125698	0	46	125744	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	255	314	0.813	0.0000169	3608
Missense in Polyphen		101	133.01	0.75932		1503
Synonymous	-0.955	127	114	1.11	0.00000645	1061
Loss of Function	2.25	15	27.8	0.540	0.00000151	341

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000912	0.0000911
Ashkenazi Jewish	0.00	0.00
East Asian	0.000335	0.000326
Finnish	0.000232	0.000231
European (Non-Finnish)	0.000233	0.000229
Middle Eastern	0.000335	0.000326
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1/SPTLC1 constitutes the catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. The SPTLC1-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, while the SPTLC1-SPTLC3-SPTSSB has the ability to use a broader range of acyl-CoAs without apparent preference. {ECO:0000269|PubMed:19416851}.
• Pathway: Sphingolipid signaling pathway - Homo sapiens (human);Sphingolipid metabolism - Homo sapiens (human);Sphingolipid Metabolism;Metabolism of lipids;Metabolism;ceramide <i>de novo</i> biosynthesis;Sphingolipid de novo biosynthesis;Sphingolipid metabolism (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.252
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.43

Haploinsufficiency Scores

• pHI: 0.105
• hipred: N
• hipred_score: 0.306
• ghis: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.520

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sptlc3

Zebrafish Information Network

• Gene name: sptlc3
• Affected structure: motor neuron
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: sphingolipid biosynthetic process;sphingoid biosynthetic process
• Cellular component: endoplasmic reticulum membrane;integral component of membrane;serine C-palmitoyltransferase complex
• Molecular function: serine C-palmitoyltransferase activity;protein binding;pyridoxal phosphate binding