SPTLC1 (serine palmitoyltransferase long chain base subunit 1)

Gene

• Entrez ID: 10558
• Gene name: Serine palmitoyltransferase long chain base subunit 1
• Gene symbol: SPTLC1
• Synonyms (NCBI Gene): ALS27, HSAN1, HSN1, LBC1, LCB1, SPT1, SPTI
• Chromosome: 9
• Chromosome location: 9q22.31
• Summary: This gene encodes a member of the class-II pyridoxal-phosphate-dependent aminotransferase family. The encoded protein is the long chain base subunit 1 of serine palmitoyltransferase. Serine palmitoyltransferase converts L-serine and palmitoyl-CoA to 3-oxo

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs119482081	C>T	Pathogenic, uncertain-significance	Coding sequence variant, genic upstream transcript variant, 5 prime UTR variant, missense variant
rs119482082	A>C	Pathogenic	Coding sequence variant, genic upstream transcript variant, 5 prime UTR variant, missense variant
rs119482083	A>T	Likely-pathogenic	Coding sequence variant, missense variant, 5 prime UTR variant, genic downstream transcript variant
rs267607087	G>A,T	Uncertain-significance, pathogenic	Missense variant, genic downstream transcript variant, coding sequence variant
rs267607088	G>A	Pathogenic	Missense variant, genic downstream transcript variant, coding sequence variant
rs797045071	C>G	Likely-pathogenic	Coding sequence variant, missense variant, genic downstream transcript variant
rs1197928094	AAG>-	Likely-pathogenic	Coding sequence variant, genic upstream transcript variant, 5 prime UTR variant, inframe deletion
rs1554716504	T>A	Likely-pathogenic	5 prime UTR variant, genic upstream transcript variant, coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT001411	hsa-miR-16-5p	pSILAC	18668040
MIRT016036	hsa-miR-374b-5p	Sequencing	20371350
MIRT023301	hsa-miR-122-5p	Microarray	17612493
MIRT001411	hsa-miR-16-5p	Proteomics;Other	18668040
MIRT049097	hsa-miR-92a-3p	CLASH	23622248
MIRT049097	hsa-miR-92a-3p	CLASH	23622248
MIRT045166	hsa-miR-186-5p	CLASH	23622248
MIRT554008	hsa-miR-4476	PAR-CLIP	21572407
MIRT554007	hsa-miR-6876-5p	PAR-CLIP	21572407
MIRT554006	hsa-miR-518c-5p	PAR-CLIP	21572407
MIRT554005	hsa-miR-326	PAR-CLIP	21572407
MIRT554004	hsa-miR-330-5p	PAR-CLIP	21572407
MIRT554003	hsa-miR-6764-3p	PAR-CLIP	21572407
MIRT554002	hsa-miR-6824-3p	PAR-CLIP	21572407
MIRT554001	hsa-miR-3191-5p	PAR-CLIP	21572407
MIRT554000	hsa-miR-1178-3p	PAR-CLIP	21572407
MIRT726462	hsa-miR-15a-5p	HITS-CLIP	22473208
MIRT726461	hsa-miR-15b-5p	HITS-CLIP	22473208
MIRT001411	hsa-miR-16-5p	HITS-CLIP	22473208
MIRT726460	hsa-miR-195-5p	HITS-CLIP	22473208
MIRT736437	hsa-miR-1-3p	Microarray	33260781
MIRT554008	hsa-miR-4476	PAR-CLIP	21572407
MIRT554007	hsa-miR-6876-5p	PAR-CLIP	21572407
MIRT554006	hsa-miR-518c-5p	PAR-CLIP	21572407
MIRT554005	hsa-miR-326	PAR-CLIP	21572407
MIRT554004	hsa-miR-330-5p	PAR-CLIP	21572407
MIRT554003	hsa-miR-6764-3p	PAR-CLIP	21572407
MIRT554002	hsa-miR-6824-3p	PAR-CLIP	21572407
MIRT554001	hsa-miR-3191-5p	PAR-CLIP	21572407
MIRT554000	hsa-miR-1178-3p	PAR-CLIP	21572407
MIRT1386968	hsa-miR-124	CLIP-seq
MIRT1386969	hsa-miR-15a	CLIP-seq
MIRT1386970	hsa-miR-15b	CLIP-seq
MIRT1386971	hsa-miR-16	CLIP-seq
MIRT1386972	hsa-miR-195	CLIP-seq
MIRT1386973	hsa-miR-2116	CLIP-seq
MIRT1386974	hsa-miR-3173-3p	CLIP-seq
MIRT1386975	hsa-miR-361-3p	CLIP-seq
MIRT1386976	hsa-miR-362-5p	CLIP-seq
MIRT1386977	hsa-miR-3650	CLIP-seq
MIRT1386978	hsa-miR-377	CLIP-seq
MIRT1386979	hsa-miR-3913-3p	CLIP-seq
MIRT1386980	hsa-miR-409-3p	CLIP-seq
MIRT1386981	hsa-miR-424	CLIP-seq
MIRT1386982	hsa-miR-4255	CLIP-seq
MIRT1386983	hsa-miR-4326	CLIP-seq
MIRT1386984	hsa-miR-4330	CLIP-seq
MIRT1386985	hsa-miR-4422	CLIP-seq
MIRT1386986	hsa-miR-4424	CLIP-seq
MIRT1386987	hsa-miR-4428	CLIP-seq
MIRT1386988	hsa-miR-4457	CLIP-seq
MIRT1386989	hsa-miR-4477b	CLIP-seq
MIRT1386990	hsa-miR-4504	CLIP-seq
MIRT1386991	hsa-miR-4521	CLIP-seq
MIRT1386992	hsa-miR-4653-3p	CLIP-seq
MIRT1386993	hsa-miR-4662a-5p	CLIP-seq
MIRT1386994	hsa-miR-4677-5p	CLIP-seq
MIRT1386995	hsa-miR-4684-3p	CLIP-seq
MIRT1386996	hsa-miR-4705	CLIP-seq
MIRT1386997	hsa-miR-4724-5p	CLIP-seq
MIRT1386998	hsa-miR-4777-3p	CLIP-seq
MIRT1386999	hsa-miR-489	CLIP-seq
MIRT1387000	hsa-miR-497	CLIP-seq
MIRT1387001	hsa-miR-500b	CLIP-seq
MIRT1387002	hsa-miR-501-5p	CLIP-seq
MIRT1387003	hsa-miR-506	CLIP-seq
MIRT1387004	hsa-miR-513b	CLIP-seq
MIRT1387005	hsa-miR-520f	CLIP-seq
MIRT1387006	hsa-miR-522	CLIP-seq
MIRT1387007	hsa-miR-542-3p	CLIP-seq
MIRT1387008	hsa-miR-548t	CLIP-seq
MIRT1387009	hsa-miR-875-5p	CLIP-seq
MIRT1387010	hsa-miR-125a-3p	CLIP-seq
MIRT1387011	hsa-miR-2052	CLIP-seq
MIRT1387012	hsa-miR-3545-3p	CLIP-seq
MIRT1387013	hsa-miR-3934	CLIP-seq
MIRT1387014	hsa-miR-4680-5p	CLIP-seq
MIRT1387015	hsa-miR-4763-5p	CLIP-seq
MIRT1387016	hsa-miR-764	CLIP-seq
MIRT2115819	hsa-miR-1207-5p	CLIP-seq
MIRT1386968	hsa-miR-124	CLIP-seq
MIRT2115820	hsa-miR-127-5p	CLIP-seq
MIRT2115821	hsa-miR-145	CLIP-seq
MIRT2115822	hsa-miR-147	CLIP-seq
MIRT1386969	hsa-miR-15a	CLIP-seq
MIRT1386970	hsa-miR-15b	CLIP-seq
MIRT1386971	hsa-miR-16	CLIP-seq
MIRT2115823	hsa-miR-181a	CLIP-seq
MIRT2115824	hsa-miR-181b	CLIP-seq
MIRT2115825	hsa-miR-181c	CLIP-seq
MIRT2115826	hsa-miR-181d	CLIP-seq
MIRT1386972	hsa-miR-195	CLIP-seq
MIRT2115827	hsa-miR-1972	CLIP-seq
MIRT1386973	hsa-miR-2116	CLIP-seq
MIRT2115828	hsa-miR-299-5p	CLIP-seq
MIRT2115829	hsa-miR-3065-5p	CLIP-seq
MIRT2115830	hsa-miR-3121-3p	CLIP-seq
MIRT2115831	hsa-miR-3183	CLIP-seq
MIRT2115832	hsa-miR-3591-5p	CLIP-seq
MIRT2115833	hsa-miR-3613-3p	CLIP-seq
MIRT1386975	hsa-miR-361-3p	CLIP-seq
MIRT1386976	hsa-miR-362-5p	CLIP-seq
MIRT1386977	hsa-miR-3650	CLIP-seq
MIRT2115834	hsa-miR-3688-5p	CLIP-seq
MIRT2115835	hsa-miR-3909	CLIP-seq
MIRT2115836	hsa-miR-3911	CLIP-seq
MIRT1386979	hsa-miR-3913-3p	CLIP-seq
MIRT2115837	hsa-miR-3925-3p	CLIP-seq
MIRT1386980	hsa-miR-409-3p	CLIP-seq
MIRT1386981	hsa-miR-424	CLIP-seq
MIRT2115838	hsa-miR-4262	CLIP-seq
MIRT2115839	hsa-miR-4294	CLIP-seq
MIRT2115840	hsa-miR-4328	CLIP-seq
MIRT1386985	hsa-miR-4422	CLIP-seq
MIRT2115841	hsa-miR-4435	CLIP-seq
MIRT1386988	hsa-miR-4457	CLIP-seq
MIRT2115842	hsa-miR-4459	CLIP-seq
MIRT1386990	hsa-miR-4504	CLIP-seq
MIRT2115843	hsa-miR-4520a-5p	CLIP-seq
MIRT2115844	hsa-miR-4520b-5p	CLIP-seq
MIRT2115845	hsa-miR-4650-5p	CLIP-seq
MIRT1386994	hsa-miR-4677-5p	CLIP-seq
MIRT2115846	hsa-miR-4695-5p	CLIP-seq
MIRT1386996	hsa-miR-4705	CLIP-seq
MIRT2115847	hsa-miR-4717-5p	CLIP-seq
MIRT2115848	hsa-miR-4722-5p	CLIP-seq
MIRT2115849	hsa-miR-4723-3p	CLIP-seq
MIRT1386997	hsa-miR-4724-5p	CLIP-seq
MIRT2115850	hsa-miR-4736	CLIP-seq
MIRT2115851	hsa-miR-4738-3p	CLIP-seq
MIRT2115852	hsa-miR-4753-3p	CLIP-seq
MIRT2115853	hsa-miR-4760-5p	CLIP-seq
MIRT2115854	hsa-miR-4763-3p	CLIP-seq
MIRT1386999	hsa-miR-489	CLIP-seq
MIRT2115855	hsa-miR-495	CLIP-seq
MIRT1387000	hsa-miR-497	CLIP-seq
MIRT1387001	hsa-miR-500b	CLIP-seq
MIRT1387002	hsa-miR-501-5p	CLIP-seq
MIRT1387003	hsa-miR-506	CLIP-seq
MIRT1387004	hsa-miR-513b	CLIP-seq
MIRT1387006	hsa-miR-522	CLIP-seq
MIRT2115856	hsa-miR-526b	CLIP-seq
MIRT1387007	hsa-miR-542-3p	CLIP-seq
MIRT2115857	hsa-miR-543	CLIP-seq
MIRT2115858	hsa-miR-548l	CLIP-seq
MIRT2115859	hsa-miR-548n	CLIP-seq
MIRT2115860	hsa-miR-564	CLIP-seq
MIRT2115861	hsa-miR-627	CLIP-seq
MIRT2115862	hsa-miR-644	CLIP-seq
MIRT2115863	hsa-miR-653	CLIP-seq
MIRT1387009	hsa-miR-875-5p	CLIP-seq
MIRT2115864	hsa-miR-924	CLIP-seq
MIRT2338380	hsa-miR-1236	CLIP-seq
MIRT1386968	hsa-miR-124	CLIP-seq
MIRT1386969	hsa-miR-15a	CLIP-seq
MIRT1386970	hsa-miR-15b	CLIP-seq
MIRT1386971	hsa-miR-16	CLIP-seq
MIRT1386972	hsa-miR-195	CLIP-seq
MIRT1386973	hsa-miR-2116	CLIP-seq
MIRT2115833	hsa-miR-3613-3p	CLIP-seq
MIRT2338381	hsa-miR-3616-5p	CLIP-seq
MIRT1386976	hsa-miR-362-5p	CLIP-seq
MIRT2338382	hsa-miR-3647-5p	CLIP-seq
MIRT1386977	hsa-miR-3650	CLIP-seq
MIRT1386978	hsa-miR-377	CLIP-seq
MIRT1386979	hsa-miR-3913-3p	CLIP-seq
MIRT1386980	hsa-miR-409-3p	CLIP-seq
MIRT1386981	hsa-miR-424	CLIP-seq
MIRT1386982	hsa-miR-4255	CLIP-seq
MIRT1386983	hsa-miR-4326	CLIP-seq
MIRT1386985	hsa-miR-4422	CLIP-seq
MIRT1386988	hsa-miR-4457	CLIP-seq
MIRT2338383	hsa-miR-4470	CLIP-seq
MIRT1386990	hsa-miR-4504	CLIP-seq
MIRT1386991	hsa-miR-4521	CLIP-seq
MIRT1386994	hsa-miR-4677-5p	CLIP-seq
MIRT1386995	hsa-miR-4684-3p	CLIP-seq
MIRT1386996	hsa-miR-4705	CLIP-seq
MIRT1386998	hsa-miR-4777-3p	CLIP-seq
MIRT2338384	hsa-miR-4781-3p	CLIP-seq
MIRT2338385	hsa-miR-4789-3p	CLIP-seq
MIRT2338386	hsa-miR-4795-5p	CLIP-seq
MIRT1386999	hsa-miR-489	CLIP-seq
MIRT1387000	hsa-miR-497	CLIP-seq
MIRT1387001	hsa-miR-500b	CLIP-seq
MIRT1387002	hsa-miR-501-5p	CLIP-seq
MIRT1387003	hsa-miR-506	CLIP-seq
MIRT1387004	hsa-miR-513b	CLIP-seq
MIRT1387006	hsa-miR-522	CLIP-seq
MIRT1387007	hsa-miR-542-3p	CLIP-seq
MIRT2338387	hsa-miR-573	CLIP-seq
MIRT2115863	hsa-miR-653	CLIP-seq
MIRT2338388	hsa-miR-875-3p	CLIP-seq
MIRT1387009	hsa-miR-875-5p	CLIP-seq
MIRT2338389	hsa-miR-877	CLIP-seq
MIRT1386973	hsa-miR-2116	CLIP-seq
MIRT1386994	hsa-miR-4677-5p	CLIP-seq
MIRT2115852	hsa-miR-4753-3p	CLIP-seq
MIRT2433525	hsa-miR-137	CLIP-seq
MIRT2433526	hsa-miR-3920	CLIP-seq
MIRT2433527	hsa-miR-4762-3p	CLIP-seq
MIRT2433528	hsa-miR-944	CLIP-seq
MIRT2460499	hsa-miR-122	CLIP-seq
MIRT2460500	hsa-miR-1307	CLIP-seq
MIRT2460501	hsa-miR-3135b	CLIP-seq
MIRT2460502	hsa-miR-3149	CLIP-seq
MIRT2460503	hsa-miR-3622b-5p	CLIP-seq
MIRT2460504	hsa-miR-3652	CLIP-seq
MIRT2460505	hsa-miR-411	CLIP-seq
MIRT2460506	hsa-miR-4284	CLIP-seq
MIRT2460507	hsa-miR-4423-5p	CLIP-seq
MIRT2460508	hsa-miR-4430	CLIP-seq
MIRT2460509	hsa-miR-4638-5p	CLIP-seq
MIRT2460510	hsa-miR-4695-3p	CLIP-seq
MIRT2460511	hsa-miR-4735-5p	CLIP-seq
MIRT2460512	hsa-miR-4772-3p	CLIP-seq
MIRT2460513	hsa-miR-4775	CLIP-seq
MIRT2460514	hsa-miR-590-3p	CLIP-seq
MIRT2115819	hsa-miR-1207-5p	CLIP-seq
MIRT2631945	hsa-miR-1238	CLIP-seq
MIRT2631946	hsa-miR-1343	CLIP-seq
MIRT2115822	hsa-miR-147	CLIP-seq
MIRT2115827	hsa-miR-1972	CLIP-seq
MIRT1386973	hsa-miR-2116	CLIP-seq
MIRT2631947	hsa-miR-3119	CLIP-seq
MIRT2631948	hsa-miR-3168	CLIP-seq
MIRT2631949	hsa-miR-3177-5p	CLIP-seq
MIRT2115831	hsa-miR-3183	CLIP-seq
MIRT2115832	hsa-miR-3591-5p	CLIP-seq
MIRT2631950	hsa-miR-3671	CLIP-seq
MIRT2115834	hsa-miR-3688-5p	CLIP-seq
MIRT2631951	hsa-miR-369-3p	CLIP-seq
MIRT2631952	hsa-miR-374a	CLIP-seq
MIRT2631953	hsa-miR-374b	CLIP-seq
MIRT2631954	hsa-miR-378g	CLIP-seq
MIRT2115835	hsa-miR-3909	CLIP-seq
MIRT2115836	hsa-miR-3911	CLIP-seq
MIRT1386979	hsa-miR-3913-3p	CLIP-seq
MIRT2631955	hsa-miR-4263	CLIP-seq
MIRT2631956	hsa-miR-4277	CLIP-seq
MIRT2631957	hsa-miR-4281	CLIP-seq
MIRT2115839	hsa-miR-4294	CLIP-seq
MIRT2115841	hsa-miR-4435	CLIP-seq
MIRT2631958	hsa-miR-4449	CLIP-seq
MIRT2115842	hsa-miR-4459	CLIP-seq
MIRT2115843	hsa-miR-4520a-5p	CLIP-seq
MIRT2115844	hsa-miR-4520b-5p	CLIP-seq
MIRT2631959	hsa-miR-4522	CLIP-seq
MIRT2631960	hsa-miR-4532	CLIP-seq
MIRT2115845	hsa-miR-4650-5p	CLIP-seq
MIRT2631961	hsa-miR-4666-3p	CLIP-seq
MIRT1386994	hsa-miR-4677-5p	CLIP-seq
MIRT2115846	hsa-miR-4695-5p	CLIP-seq
MIRT2115847	hsa-miR-4717-5p	CLIP-seq
MIRT2115848	hsa-miR-4722-5p	CLIP-seq
MIRT2115849	hsa-miR-4723-3p	CLIP-seq
MIRT2115850	hsa-miR-4736	CLIP-seq
MIRT2115852	hsa-miR-4753-3p	CLIP-seq
MIRT2115853	hsa-miR-4760-5p	CLIP-seq
MIRT2115854	hsa-miR-4763-3p	CLIP-seq
MIRT1386999	hsa-miR-489	CLIP-seq
MIRT2631962	hsa-miR-518a-5p	CLIP-seq
MIRT2115856	hsa-miR-526b	CLIP-seq
MIRT2631963	hsa-miR-527	CLIP-seq
MIRT2631964	hsa-miR-548c-3p	CLIP-seq
MIRT2631965	hsa-miR-561	CLIP-seq
MIRT2631966	hsa-miR-576-3p	CLIP-seq
MIRT2631967	hsa-miR-607	CLIP-seq
MIRT2631968	hsa-miR-616	CLIP-seq
MIRT2115861	hsa-miR-627	CLIP-seq
MIRT2115862	hsa-miR-644	CLIP-seq
MIRT2631969	hsa-miR-648	CLIP-seq
MIRT2115864	hsa-miR-924	CLIP-seq
MIRT2115819	hsa-miR-1207-5p	CLIP-seq
MIRT2631945	hsa-miR-1238	CLIP-seq
MIRT2631946	hsa-miR-1343	CLIP-seq
MIRT2115822	hsa-miR-147	CLIP-seq
MIRT2115827	hsa-miR-1972	CLIP-seq
MIRT1386973	hsa-miR-2116	CLIP-seq
MIRT2631947	hsa-miR-3119	CLIP-seq
MIRT2631948	hsa-miR-3168	CLIP-seq
MIRT2631949	hsa-miR-3177-5p	CLIP-seq
MIRT2115831	hsa-miR-3183	CLIP-seq
MIRT2691939	hsa-miR-34b	CLIP-seq
MIRT2115832	hsa-miR-3591-5p	CLIP-seq
MIRT2631950	hsa-miR-3671	CLIP-seq
MIRT2115834	hsa-miR-3688-5p	CLIP-seq
MIRT2631951	hsa-miR-369-3p	CLIP-seq
MIRT2631952	hsa-miR-374a	CLIP-seq
MIRT2631953	hsa-miR-374b	CLIP-seq
MIRT2631954	hsa-miR-378g	CLIP-seq
MIRT2115835	hsa-miR-3909	CLIP-seq
MIRT2115836	hsa-miR-3911	CLIP-seq
MIRT1386979	hsa-miR-3913-3p	CLIP-seq
MIRT2631955	hsa-miR-4263	CLIP-seq
MIRT2631956	hsa-miR-4277	CLIP-seq
MIRT2631957	hsa-miR-4281	CLIP-seq
MIRT2115839	hsa-miR-4294	CLIP-seq
MIRT2115841	hsa-miR-4435	CLIP-seq
MIRT2631958	hsa-miR-4449	CLIP-seq
MIRT2115842	hsa-miR-4459	CLIP-seq
MIRT2115843	hsa-miR-4520a-5p	CLIP-seq
MIRT2115844	hsa-miR-4520b-5p	CLIP-seq
MIRT2631959	hsa-miR-4522	CLIP-seq
MIRT2631960	hsa-miR-4532	CLIP-seq
MIRT2115845	hsa-miR-4650-5p	CLIP-seq
MIRT2631961	hsa-miR-4666-3p	CLIP-seq
MIRT1386994	hsa-miR-4677-5p	CLIP-seq
MIRT2115846	hsa-miR-4695-5p	CLIP-seq
MIRT2115847	hsa-miR-4717-5p	CLIP-seq
MIRT2115848	hsa-miR-4722-5p	CLIP-seq
MIRT2115849	hsa-miR-4723-3p	CLIP-seq
MIRT2115850	hsa-miR-4736	CLIP-seq
MIRT2115852	hsa-miR-4753-3p	CLIP-seq
MIRT2115853	hsa-miR-4760-5p	CLIP-seq
MIRT2115854	hsa-miR-4763-3p	CLIP-seq
MIRT1386999	hsa-miR-489	CLIP-seq
MIRT2631962	hsa-miR-518a-5p	CLIP-seq
MIRT2115856	hsa-miR-526b	CLIP-seq
MIRT2631963	hsa-miR-527	CLIP-seq
MIRT2631964	hsa-miR-548c-3p	CLIP-seq
MIRT2631965	hsa-miR-561	CLIP-seq
MIRT2631966	hsa-miR-576-3p	CLIP-seq
MIRT2631967	hsa-miR-607	CLIP-seq
MIRT2631968	hsa-miR-616	CLIP-seq
MIRT2115861	hsa-miR-627	CLIP-seq
MIRT2115862	hsa-miR-644	CLIP-seq
MIRT2631969	hsa-miR-648	CLIP-seq
MIRT2115864	hsa-miR-924	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0004758	Function	Serine C-palmitoyltransferase activity	IBA
GO:0004758	Function	Serine C-palmitoyltransferase activity	IDA	25332431, 25691431
GO:0004758	Function	Serine C-palmitoyltransferase activity	IDA	19416851
GO:0004758	Function	Serine C-palmitoyltransferase activity	IEA
GO:0004758	Function	Serine C-palmitoyltransferase activity	TAS	9363775
GO:0005515	Function	Protein binding	IPI	19416851, 20182505, 32814053, 33558761, 35271311
GO:0005783	Component	Endoplasmic reticulum	IBA
GO:0005783	Component	Endoplasmic reticulum	IDA
GO:0005783	Component	Endoplasmic reticulum	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	NAS	33558761
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006665	Process	Sphingolipid metabolic process	IEA
GO:0006665	Process	Sphingolipid metabolic process	TAS	9363775
GO:0006686	Process	Sphingomyelin biosynthetic process	IEA
GO:0016020	Component	Membrane	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016746	Function	Acyltransferase activity	IEA
GO:0017059	Component	Serine palmitoyltransferase complex	IDA	19416851, 20182505, 25691431
GO:0017059	Component	Serine palmitoyltransferase complex	IPI	19416851, 33558761
GO:0030148	Process	Sphingolipid biosynthetic process	IDA	25332431
GO:0030148	Process	Sphingolipid biosynthetic process	IEA
GO:0030148	Process	Sphingolipid biosynthetic process	TAS	19416851
GO:0030170	Function	Pyridoxal phosphate binding	IEA
GO:0043604	Process	Amide biosynthetic process	IEA
GO:0046511	Process	Sphinganine biosynthetic process	IEA
GO:0046512	Process	Sphingosine biosynthetic process	IBA
GO:0046512	Process	Sphingosine biosynthetic process	IDA	19416851, 33558761
GO:0046512	Process	Sphingosine biosynthetic process	IEA
GO:0046513	Process	Ceramide biosynthetic process	IBA
GO:0046513	Process	Ceramide biosynthetic process	IDA	25691431
GO:0046513	Process	Ceramide biosynthetic process	IEA
GO:1904504	Process	Positive regulation of lipophagy	IDA	25332431
GO:1904649	Process	Regulation of fat cell apoptotic process	IEA
GO:1904649	Process	Regulation of fat cell apoptotic process	ISS

Other IDs

• MIM: 605712
• HGNC: 11277
• e!Ensembl: ENSG00000090054

Protein

• UniProt ID: O15269
• Protein name: Serine palmitoyltransferase 1 (EC 2.3.1.50) (Long chain base biosynthesis protein 1) (LCB 1) (Serine-palmitoyl-CoA transferase 1) (SPT 1) (SPT1)
• Protein function: Component of the serine palmitoyltransferase multisubunit enzyme (SPT) that catalyzes the initial and rate-limiting step in sphingolipid biosynthesis by condensing L-serine and activated acyl-CoA (most commonly palmitoyl-CoA) to form long-chain
• PDB: 6M4N, 6M4O, 7CQI, 7CQK, 7K0I, 7K0J, 7K0K, 7K0L, 7K0M, 7K0N, 7K0O, 7K0P, 7K0Q, 7YIU, 7YIY, 7YJ1, 7YJ2
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00155	Aminotran_1_2	98 → 464	Aminotransferase class I and II	Domain

• Tissue specificity: TISSUE SPECIFICITY: Widely expressed. Not detected in small intestine. {ECO:0000269|PubMed:17023427}.
• Sequence:

  MATATEQWVLVEMVQALYEAPAYHLILEGILILWIIRLLFSKTYKLQERSDLTVKEKEEL
  IEEWQPEPLVPPVPKDHPALNYNIVSGPPSHKTVVNGKECINFASFNFLGLLDNPRVKAA
  ALASLKKYGVGTCGPRGFYGTFDVHLDLEDRLAKFMKTEEAIIYSYGFATIASAIPAYSK
  RGDIVFVDRAACFAIQKGLQASRSDIKLFKHNDMADLERLLKEQEIEDQKNPRKARVTRR
  FIVVEGLYMNTGTICPLPELVKLKYKYKARIFLEESLSFGVLGEHGRGVTEHYGINIDDI
  DLISANMENALASIGGFCCGRSFVIDHQRLSGQGYCFSASLPPLLAAAAIEALNIMEENP
  GIFAVLKEKCGQIHKALQGISGLKVVGESLSPAFHLQLEESTGSREQDVRLLQEIVDQCM
  NRSIALTQARYLEKEEKCLPPPSIRVVVTVEQTEEELERAASTIKEVAQAVLL

• Sequence length: 473

Pathways

KEGG:

Sphingolipid metabolism
Metabolic pathways
Sphingolipid signaling pathway

Reactome:

Sphingolipid de novo biosynthesis

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Amyotrophic lateral sclerosis	Likely pathogenic	rs2118840030	RCV001579316	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Amyotrophic lateral sclerosis 27, juvenile	Pathogenic; Likely pathogenic	rs1478177125, rs879254294, rs267607087, rs1554716504, rs1197928094, rs2118840030	RCV003152660 RCV003223342 RCV003152600 RCV003152607 RCV003152613 RCV003152625	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Charcot-Marie-Tooth disease	Pathogenic; Likely pathogenic	rs119482081, rs119482083, rs119482082, rs267607087	RCV001027483 RCV001174070 RCV001174071 RCV000790228	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
EMG abnormality	Likely pathogenic; Pathogenic	rs1197928094	RCV002468610	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Falls	Likely pathogenic; Pathogenic	rs1197928094	RCV002468610	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hereditary sensory and autonomic neuropathy type 1	Likely pathogenic; Pathogenic	rs119482081, rs119482083, rs119482082, rs797045071, rs267607087, rs1554706429, rs1197928094	RCV002601672 RCV000005067 RCV000005068 RCV000005070 RCV000191132 RCV000795948 RCV000557521 RCV001858688	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Muscle spasm	Likely pathogenic; Pathogenic	rs1197928094	RCV002468610	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neuropathy, hereditary sensory and autonomic, type 1A	Likely pathogenic; Pathogenic	rs2118448441, rs119482081, rs119482083, rs119482082, rs267607087, rs879254294, rs1554716504, rs1197928094	RCV001754569 RCV001249800 RCV001249799 RCV001249798 RCV003223389 RCV004594033 RCV001267702 RCV000988188	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Neuropathy, hereditary sensory and autonomic, type IA, severe	Pathogenic	rs267607087	RCV000005071 RCV001249813	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Proximal lower limb amyotrophy	Likely pathogenic; Pathogenic	rs1197928094	RCV002468610	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Proximal muscle weakness	Likely pathogenic; Pathogenic	rs1197928094	RCV002468610	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Ritscher-Schinzel syndrome 4	Pathogenic	rs879254294	RCV005860050	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Sensorimotor neuropathy	Pathogenic	rs119482082	RCV001004021	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SPTLC1-related disorder	Likely pathogenic; Pathogenic	rs119482083	RCV004755711	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ALZHEIMER'S DISEASE NEUROPATHOLOGIC CHANGE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BIPOLAR DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Childhood onset hearing loss	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEMENTIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLAUCOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEREDITARY SENSORY AUTONOMIC NEUROPATHY TYPE IA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEREDITARY SENSORY AUTONOMIC NEUROPATHY, TYPE 1	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
JUVENILE AMYOTROPHIC LATERAL SCLEROSIS	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MENTAL OR BEHAVIOURAL DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microcephaly	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE IA	—	CTD, HPO CTD, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Amyotrophic Lateral Sclerosis	Amyotrophic lateral sclerosis	Pubtator	34059824, 34459874, 35627278, 36966328, 38041684	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Amyotrophic Lateral Sclerosis 2 Juvenile	Amyotrophic lateral sclerosis	Pubtator	34459874, 36966328	Associate	★☆☆☆☆ Found in Text Mining only
Autonomic nervous system disorders	Autonomic Central Nervous System Diseases	BEFREE	20692858		★☆☆☆☆ Found in Text Mining only
Bipolar Disorder	Bipolar Disorder	GWASCAT_DG	22688191		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Brain Neoplasms	Brain Neoplasms	BEFREE	16968971		★☆☆☆☆ Found in Text Mining only
Brain Neoplasms	Brain neoplasms	Pubtator	16968971	Associate	★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	Pubtator	23454272	Associate	★☆☆☆☆ Found in Text Mining only
Charcot-Marie-Tooth Disease	Charcot-Marie-Tooth Disease	BEFREE	15367861		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Charcot-Marie-Tooth Disease	Charcot-Marie-Tooth Disease	GENOMICS_ENGLAND_DG	30420926		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2B (disorder)	Charcot-Marie-Tooth Disease	BEFREE	11801401, 15319794, 15455439		★☆☆☆☆ Found in Text Mining only
Chronic axonal neuropathy	Neuropathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cognition Disorders	Cognition disorder	Pubtator	35627278	Associate	★☆☆☆☆ Found in Text Mining only
Conventional (Clear Cell) Renal Cell Carcinoma	Renal Carcinoma	BEFREE	31512789, 31554600		★☆☆☆☆ Found in Text Mining only
Coronary Artery Disease	Coronary artery disease	Pubtator	37298446	Associate	★☆☆☆☆ Found in Text Mining only
Dementia	Dementia	BEFREE	22328086, 23365052		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dementia	Dementia	Pubtator	23365052	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Diabetes Mellitus	Diabetes mellitus	Pubtator	35184720	Stimulate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Non-Insulin-Dependent	Diabetes Mellitus	BEFREE	29960730		★☆☆☆☆ Found in Text Mining only
Dysautonomia	Dysautonomia	BEFREE	20692858		★☆☆☆☆ Found in Text Mining only
Dysautonomia, Familial	Dysautonomia	GENOMICS_ENGLAND_DG	30420926		★☆☆☆☆ Found in Text Mining only
Foot osteomyelitis	Foot osteomyelitis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Frontotemporal dementia	Frontotemporal dementia	BEFREE	23365052		★☆☆☆☆ Found in Text Mining only
Generalized amyotrophy	Amyotrophy	BEFREE	23454272		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	BEFREE	16968971		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	16968971	Associate	★☆☆☆☆ Found in Text Mining only
Growth Disorders	Growth disorder	Pubtator	23454272	Associate	★☆☆☆☆ Found in Text Mining only
Hearing Loss	Hearing loss	Pubtator	23365052, 34837038	Associate	★☆☆☆☆ Found in Text Mining only
Heart Valve Diseases	Heart valve disease	Pubtator	37298446	Associate	★☆☆☆☆ Found in Text Mining only
Hereditary Motor and Sensory Neuropathies	Hereditary motor and sensory neuropathy	BEFREE	11801401, 21194679		★☆☆☆☆ Found in Text Mining only
Hereditary Motor and Sensory-Neuropathy Type II	Dysautonomia	GENOMICS_ENGLAND_DG	16216550, 20097765		★☆☆☆☆ Found in Text Mining only
Hereditary Motor and Sensory-Neuropathy Type II	Dysautonomia	BEFREE	9219740		★☆☆☆☆ Found in Text Mining only
Hereditary Sensory and Autonomic Neuropathies	Hereditary sensory and autonomic neuropathy	Pubtator	11479835, 14990347, 19651702, 21618344, 22302274, 23454272, 24175284, 25567748, 26681808, 34059824, 34337561, 34459874, 35627278, 35904184, 37107689	Associate	★☆☆☆☆ Found in Text Mining only
Hereditary Sensory and Autonomic Neuropathies	Hereditary sensory and autonomic neuropathy	BEFREE	15367861, 19183217, 19651702, 20692858, 26573920		★☆☆☆☆ Found in Text Mining only
Hereditary sensory and autonomic neuropathy type 1	Sensory And Autonomic Neuropathy	Orphanet			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Hereditary Sensory Autonomic Neuropathy, Type 1	Hereditary sensory and autonomic neuropathy	BEFREE	10025779, 10942106, 11242114, 11479835, 11801401, 12417569, 12870133, 14990347, 15037712, 15367861, 15455439, 15546589, 16271825, 18348718, 20097765, 20504773, 21194679, 21618344, 22045570, 23454272, 24247255, 29778900, 30866134, 30995999, 8673084, 9219740, 9465296, 9722951		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hereditary Sensory Autonomic Neuropathy, Type 1	Hereditary sensory and autonomic neuropathy	GENOMICS_ENGLAND_DG	11242106, 11242114, 16216550, 19132419, 20097765		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hereditary Sensory Autonomic Neuropathy, Type 1	Hereditary sensory and autonomic neuropathy	CLINVAR_DG	11242106, 11242114, 12417569, 16210380, 16364956, 18018475, 19132419, 19651702, 19923297, 20097765, 21618344, 22302274, 23454272, 24247255, 24673574, 25584079, 26633545, 26681808		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hereditary Sensory Autonomic Neuropathy, Type 1	Hereditary sensory and autonomic neuropathy	UNIPROT_DG	11242114, 19132419, 19651702, 20504773, 21618344, 22302274, 24247255, 30420926		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hereditary Sensory Autonomic Neuropathy, Type 1	Hereditary sensory and autonomic neuropathy	ORPHANET_DG	11242114		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hereditary Sensory Autonomic Neuropathy, Type 1	Hereditary sensory and autonomic neuropathy	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hereditary Sensory Radicular Neuropathy	Hereditary sensory and autonomic neuropathy	BEFREE	12207934, 8673084		★☆☆☆☆ Found in Text Mining only
Huntington Disease	Huntington Disease	BEFREE	29311779		★☆☆☆☆ Found in Text Mining only
Hyperkeratosis	Hyperkeratosis	BEFREE	12207934		★☆☆☆☆ Found in Text Mining only
Keratosis	Keratosis	BEFREE	12207934		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of brain	Brain Neoplasms	BEFREE	16968971		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	UNIPROT_DG			★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	9169137, 9465296		★☆☆☆☆ Found in Text Mining only
Mental disorders	Mental Disorders	GWASDB_DG	22688191		★☆☆☆☆ Found in Text Mining only
Motor Neuron Disease	Motor neuron disease	Pubtator	35904184, 38041684	Associate	★☆☆☆☆ Found in Text Mining only
Multiple self-healing squamous epithelioma	Multiple Self-Healing Epithelioma	BEFREE	9722951		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	31512789, 31554600		★☆☆☆☆ Found in Text Mining only
Nervous System Diseases	Nervous system disease	Pubtator	34103343, 35627278	Associate	★☆☆☆☆ Found in Text Mining only
nervous system disorder	Nervous System Disorder	BEFREE	18348718, 30952607, 9169137		★☆☆☆☆ Found in Text Mining only
Neurodegenerative Diseases	Neurodegenerative disorder	Pubtator	14990347	Associate	★☆☆☆☆ Found in Text Mining only
Neurodegenerative Disorders	Neurodegenerative Disorders	BEFREE	19132419		★☆☆☆☆ Found in Text Mining only
Neuropathy	Neuropathy	BEFREE	11801401, 15367861, 15455439, 15965219, 16364956, 30995999		★☆☆☆☆ Found in Text Mining only
Obesity	Obesity	Pubtator	35184720	Associate	★☆☆☆☆ Found in Text Mining only
Peripheral Nervous System Diseases	Nervous System Diseases	BEFREE	11801401, 15037712, 29778900, 9722951		★☆☆☆☆ Found in Text Mining only
Peripheral Nervous System Diseases	Peripheral nervous system disease	Pubtator	35904184, 37107689	Associate	★☆☆☆☆ Found in Text Mining only
Peripheral Neuropathy	Peripheral Neuropathy	BEFREE	11801401, 29778900, 9722951		★☆☆☆☆ Found in Text Mining only
Peripheral Neuropathy	Peripheral Neuropathy	LHGDN	16210380		★☆☆☆☆ Found in Text Mining only
Presenile dementia	Senile Dementia	BEFREE	22328086, 23365052		★☆☆☆☆ Found in Text Mining only
Psychotic Disorders	Psychosis	GWASDB_DG	22688191		★☆☆☆☆ Found in Text Mining only
Renal Cell Carcinoma	Renal Carcinoma	BEFREE	31554600		★☆☆☆☆ Found in Text Mining only
Retinal Diseases	Retinal detachment	Pubtator	37107689	Associate	★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	GWASCAT_DG	22688191		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sensorimotor neuropathy	Sensorimotor neuropathy	BEFREE	11479835		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Sensorimotor neuropathy	Sensorimotor neuropathy	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Sensorineural Hearing Loss (disorder)	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Sensory neuropathy	Sensory neuropathy	BEFREE	20504773		★☆☆☆☆ Found in Text Mining only
Sensory Neuropathy, Hereditary	Sensory Neuropathy, Hereditary	BEFREE	12207934, 12633143, 15319794, 16311270, 22328086		★☆☆☆☆ Found in Text Mining only