Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	51091
Gene name Gene Name - the full gene name approved by the HGNC.	Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	SEPSECS
Synonyms (NCBI Gene) Gene synonyms aliases	LP, PCH2D, SLA, SLA-p35, SLA/LP, SecS
Chromosome Chromosome number	4
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	4p15.2
Summary Summary of gene provided in NCBI Entrez Gene.	The amino acid selenocysteine is the only amino acid that does not have its own tRNA synthetase. Instead, this amino acid is synthesized on its cognate tRNA in a three step process. The protein encoded by this gene catalyzes the third step in the process,

Show/Hide all(14)

SNP ID	Visualize variation	Clinical significance	Consequence
rs146539065	C>T	Likely-pathogenic	Synonymous variant, coding sequence variant
rs267607035	C>T	Pathogenic	Coding sequence variant, missense variant
rs267607036	T>C	Pathogenic	Coding sequence variant, missense variant
rs757504141	T>C	Likely-pathogenic	Intron variant
rs773876739	T>A,C	Pathogenic	Coding sequence variant, missense variant
rs776969714	->C	Pathogenic, pathogenic-likely-pathogenic	Coding sequence variant, splice acceptor variant
rs779387647	C>A	Likely-pathogenic	Stop gained, coding sequence variant
rs1057518887	C>T	Likely-pathogenic	Intron variant
rs1309003036	G>A,C	Pathogenic	Missense variant, stop gained, coding sequence variant, 5 prime UTR variant
rs1553878395	AAAGATATGGGATTGTGAGGTGTATGCAACAGTCTTTCATTGTAGGCTTCTGACAACTTCTTTATTTGGTTGGACAAATATGAAAACATTTCCT>-	Likely-pathogenic	Splice acceptor variant, splice donor variant, coding sequence variant
rs1553881510	->T	Pathogenic	Coding sequence variant, frameshift variant
rs1553881788	T>C	Likely-pathogenic	5 prime UTR variant, coding sequence variant, missense variant
rs1577599764	C>A	Likely-pathogenic	Splice acceptor variant
rs1577629146	GA>-	Likely-pathogenic	Frameshift variant, coding sequence variant

Show/Hide all(199)

miRTarBase ID	miRNA	Experiments	Reference
MIRT048507	hsa-miR-100-5p	CLASH	23622248
MIRT653947	hsa-miR-548c-3p	HITS-CLIP	23824327
MIRT653946	hsa-miR-1264	HITS-CLIP	23824327
MIRT653945	hsa-miR-216a-5p	HITS-CLIP	23824327
MIRT653944	hsa-miR-513c-5p	HITS-CLIP	23824327
MIRT653943	hsa-miR-514b-5p	HITS-CLIP	23824327
MIRT653947	hsa-miR-548c-3p	HITS-CLIP	23824327
MIRT653946	hsa-miR-1264	HITS-CLIP	23824327
MIRT653945	hsa-miR-216a-5p	HITS-CLIP	23824327
MIRT653944	hsa-miR-513c-5p	HITS-CLIP	23824327
MIRT653943	hsa-miR-514b-5p	HITS-CLIP	23824327
MIRT1336447	hsa-miR-1261	CLIP-seq
MIRT1336448	hsa-miR-1279	CLIP-seq
MIRT1336449	hsa-miR-1287	CLIP-seq
MIRT1336450	hsa-miR-1587	CLIP-seq
MIRT1336451	hsa-miR-2053	CLIP-seq
MIRT1336452	hsa-miR-216a	CLIP-seq
MIRT1336453	hsa-miR-29a	CLIP-seq
MIRT1336454	hsa-miR-29b	CLIP-seq
MIRT1336455	hsa-miR-29c	CLIP-seq
MIRT1336456	hsa-miR-3163	CLIP-seq
MIRT1336457	hsa-miR-3174	CLIP-seq
MIRT1336458	hsa-miR-3176	CLIP-seq
MIRT1336459	hsa-miR-320a	CLIP-seq
MIRT1336460	hsa-miR-320b	CLIP-seq
MIRT1336461	hsa-miR-320c	CLIP-seq
MIRT1336462	hsa-miR-320d	CLIP-seq
MIRT1336463	hsa-miR-3613-3p	CLIP-seq
MIRT1336464	hsa-miR-3620	CLIP-seq
MIRT1336465	hsa-miR-3647-3p	CLIP-seq
MIRT1336466	hsa-miR-3652	CLIP-seq
MIRT1336467	hsa-miR-3662	CLIP-seq
MIRT1336468	hsa-miR-3663-3p	CLIP-seq
MIRT1336469	hsa-miR-3922-3p	CLIP-seq
MIRT1336470	hsa-miR-3978	CLIP-seq
MIRT1336471	hsa-miR-425	CLIP-seq
MIRT1336472	hsa-miR-4261	CLIP-seq
MIRT1336473	hsa-miR-4429	CLIP-seq
MIRT1336474	hsa-miR-4430	CLIP-seq
MIRT1336475	hsa-miR-4492	CLIP-seq
MIRT1336476	hsa-miR-4498	CLIP-seq
MIRT1336477	hsa-miR-4656	CLIP-seq
MIRT1336478	hsa-miR-4668-3p	CLIP-seq
MIRT1336479	hsa-miR-4674	CLIP-seq
MIRT1336480	hsa-miR-4675	CLIP-seq
MIRT1336481	hsa-miR-4741	CLIP-seq
MIRT1336482	hsa-miR-4757-5p	CLIP-seq
MIRT1336483	hsa-miR-4765	CLIP-seq
MIRT1336484	hsa-miR-4777-5p	CLIP-seq
MIRT1336485	hsa-miR-494	CLIP-seq
MIRT1336486	hsa-miR-501-3p	CLIP-seq
MIRT1336487	hsa-miR-502-3p	CLIP-seq
MIRT1336488	hsa-miR-513c	CLIP-seq
MIRT1336489	hsa-miR-520d-5p	CLIP-seq
MIRT1336490	hsa-miR-524-5p	CLIP-seq
MIRT1336491	hsa-miR-569	CLIP-seq
MIRT1336492	hsa-miR-570	CLIP-seq
MIRT1336493	hsa-miR-576-3p	CLIP-seq
MIRT1336494	hsa-miR-605	CLIP-seq
MIRT1336495	hsa-miR-633	CLIP-seq
MIRT1336496	hsa-miR-762	CLIP-seq
MIRT1336497	hsa-miR-767-5p	CLIP-seq
MIRT1336498	hsa-miR-935	CLIP-seq
MIRT1553325	hsa-miR-944	CLIP-seq
MIRT2099535	hsa-miR-1202	CLIP-seq
MIRT1336447	hsa-miR-1261	CLIP-seq
MIRT1336448	hsa-miR-1279	CLIP-seq
MIRT2099536	hsa-miR-223	CLIP-seq
MIRT2099537	hsa-miR-3128	CLIP-seq
MIRT1336456	hsa-miR-3163	CLIP-seq
MIRT2099538	hsa-miR-3164	CLIP-seq
MIRT2099539	hsa-miR-3194-5p	CLIP-seq
MIRT2099540	hsa-miR-338-3p	CLIP-seq
MIRT1336463	hsa-miR-3613-3p	CLIP-seq
MIRT2099541	hsa-miR-374c	CLIP-seq
MIRT2099542	hsa-miR-3972	CLIP-seq
MIRT2099543	hsa-miR-4276	CLIP-seq
MIRT2099544	hsa-miR-4282	CLIP-seq
MIRT2099545	hsa-miR-4310	CLIP-seq
MIRT2099546	hsa-miR-4494	CLIP-seq
MIRT2099547	hsa-miR-451b	CLIP-seq
MIRT2099548	hsa-miR-4697-3p	CLIP-seq
MIRT2099549	hsa-miR-4717-3p	CLIP-seq
MIRT2099550	hsa-miR-4753-3p	CLIP-seq
MIRT2099551	hsa-miR-4793-3p	CLIP-seq
MIRT2099552	hsa-miR-499a-5p	CLIP-seq
MIRT2099553	hsa-miR-548ae	CLIP-seq
MIRT2099554	hsa-miR-548aj	CLIP-seq
MIRT2099555	hsa-miR-548am	CLIP-seq
MIRT2099556	hsa-miR-548x	CLIP-seq
MIRT2099557	hsa-miR-655	CLIP-seq
MIRT2099558	hsa-miR-888	CLIP-seq
MIRT2099559	hsa-miR-942	CLIP-seq
MIRT1336447	hsa-miR-1261	CLIP-seq
MIRT1336448	hsa-miR-1279	CLIP-seq
MIRT1336449	hsa-miR-1287	CLIP-seq
MIRT1336450	hsa-miR-1587	CLIP-seq
MIRT2324181	hsa-miR-204	CLIP-seq
MIRT2324182	hsa-miR-211	CLIP-seq
MIRT2324183	hsa-miR-2114	CLIP-seq
MIRT1336453	hsa-miR-29a	CLIP-seq
MIRT1336454	hsa-miR-29b	CLIP-seq
MIRT1336455	hsa-miR-29c	CLIP-seq
MIRT2324184	hsa-miR-3065-3p	CLIP-seq
MIRT2324185	hsa-miR-30a	CLIP-seq
MIRT2324186	hsa-miR-30b	CLIP-seq
MIRT2324187	hsa-miR-30c	CLIP-seq
MIRT2324188	hsa-miR-30d	CLIP-seq
MIRT2324189	hsa-miR-30e	CLIP-seq
MIRT2324190	hsa-miR-3140-5p	CLIP-seq
MIRT1336456	hsa-miR-3163	CLIP-seq
MIRT2324191	hsa-miR-3187-3p	CLIP-seq
MIRT2324192	hsa-miR-3607-3p	CLIP-seq
MIRT1336463	hsa-miR-3613-3p	CLIP-seq
MIRT1336466	hsa-miR-3652	CLIP-seq
MIRT1336468	hsa-miR-3663-3p	CLIP-seq
MIRT2324193	hsa-miR-3677-5p	CLIP-seq
MIRT2324194	hsa-miR-3686	CLIP-seq
MIRT2324195	hsa-miR-3913-3p	CLIP-seq
MIRT2324196	hsa-miR-3929	CLIP-seq
MIRT2324197	hsa-miR-4263	CLIP-seq
MIRT2099544	hsa-miR-4282	CLIP-seq
MIRT2324198	hsa-miR-4293	CLIP-seq
MIRT2324199	hsa-miR-4419b	CLIP-seq
MIRT2324200	hsa-miR-4427	CLIP-seq
MIRT1336474	hsa-miR-4430	CLIP-seq
MIRT2324201	hsa-miR-4478	CLIP-seq
MIRT1336475	hsa-miR-4492	CLIP-seq
MIRT1336476	hsa-miR-4498	CLIP-seq
MIRT2324202	hsa-miR-4524	CLIP-seq
MIRT2324203	hsa-miR-4529-5p	CLIP-seq
MIRT2324204	hsa-miR-4540	CLIP-seq
MIRT1336477	hsa-miR-4656	CLIP-seq
MIRT1336478	hsa-miR-4668-3p	CLIP-seq
MIRT1336479	hsa-miR-4674	CLIP-seq
MIRT1336480	hsa-miR-4675	CLIP-seq
MIRT2324205	hsa-miR-4676-5p	CLIP-seq
MIRT2324206	hsa-miR-4690-5p	CLIP-seq
MIRT2324207	hsa-miR-4713-5p	CLIP-seq
MIRT2324208	hsa-miR-4714-3p	CLIP-seq
MIRT1336481	hsa-miR-4741	CLIP-seq
MIRT2324209	hsa-miR-4755-5p	CLIP-seq
MIRT2324210	hsa-miR-489	CLIP-seq
MIRT2324211	hsa-miR-496	CLIP-seq
MIRT1336486	hsa-miR-501-3p	CLIP-seq
MIRT1336487	hsa-miR-502-3p	CLIP-seq
MIRT1336488	hsa-miR-513c	CLIP-seq
MIRT2324212	hsa-miR-575	CLIP-seq
MIRT2324213	hsa-miR-576-5p	CLIP-seq
MIRT1336494	hsa-miR-605	CLIP-seq
MIRT2324214	hsa-miR-623	CLIP-seq
MIRT1336496	hsa-miR-762	CLIP-seq
MIRT1336497	hsa-miR-767-5p	CLIP-seq
MIRT2324215	hsa-miR-802	CLIP-seq
MIRT1336447	hsa-miR-1261	CLIP-seq
MIRT1336449	hsa-miR-1287	CLIP-seq
MIRT1336450	hsa-miR-1587	CLIP-seq
MIRT2099540	hsa-miR-338-3p	CLIP-seq
MIRT1336466	hsa-miR-3652	CLIP-seq
MIRT1336474	hsa-miR-4430	CLIP-seq
MIRT1336475	hsa-miR-4492	CLIP-seq
MIRT1336476	hsa-miR-4498	CLIP-seq
MIRT1336477	hsa-miR-4656	CLIP-seq
MIRT1336479	hsa-miR-4674	CLIP-seq
MIRT1336480	hsa-miR-4675	CLIP-seq
MIRT1336481	hsa-miR-4741	CLIP-seq
MIRT1336496	hsa-miR-762	CLIP-seq
MIRT2620081	hsa-miR-3065-5p	CLIP-seq
MIRT2324193	hsa-miR-3677-5p	CLIP-seq
MIRT2620082	hsa-miR-3923	CLIP-seq
MIRT2620083	hsa-miR-3941	CLIP-seq
MIRT2620084	hsa-miR-4643	CLIP-seq
MIRT2620085	hsa-miR-466	CLIP-seq
MIRT2620086	hsa-miR-4672	CLIP-seq
MIRT2620087	hsa-miR-4789-3p	CLIP-seq
MIRT2620088	hsa-miR-495	CLIP-seq
MIRT1336488	hsa-miR-513c	CLIP-seq
MIRT2620089	hsa-miR-628-3p	CLIP-seq
MIRT2324215	hsa-miR-802	CLIP-seq
MIRT2690417	hsa-miR-1258	CLIP-seq
MIRT2690418	hsa-miR-186	CLIP-seq
MIRT2620081	hsa-miR-3065-5p	CLIP-seq
MIRT2690419	hsa-miR-3133	CLIP-seq
MIRT2324193	hsa-miR-3677-5p	CLIP-seq
MIRT2690420	hsa-miR-383	CLIP-seq
MIRT2620082	hsa-miR-3923	CLIP-seq
MIRT2620083	hsa-miR-3941	CLIP-seq
MIRT2620084	hsa-miR-4643	CLIP-seq
MIRT2620085	hsa-miR-466	CLIP-seq
MIRT2620086	hsa-miR-4672	CLIP-seq
MIRT2690421	hsa-miR-4772-5p	CLIP-seq
MIRT2690422	hsa-miR-4778-5p	CLIP-seq
MIRT2620087	hsa-miR-4789-3p	CLIP-seq
MIRT2690423	hsa-miR-4790-3p	CLIP-seq
MIRT2620088	hsa-miR-495	CLIP-seq
MIRT1336488	hsa-miR-513c	CLIP-seq
MIRT2690424	hsa-miR-553	CLIP-seq
MIRT2620089	hsa-miR-628-3p	CLIP-seq
MIRT2324215	hsa-miR-802	CLIP-seq

Show/Hide all(18)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000049	Function	TRNA binding	IBA
GO:0000049	Function	TRNA binding	IEA
GO:0000049	Function	TRNA binding	ISS
GO:0000049	Function	TRNA binding	TAS	10801173
GO:0001514	Process	Selenocysteine incorporation	IBA
GO:0001514	Process	Selenocysteine incorporation	IEA
GO:0001514	Process	Selenocysteine incorporation	ISS
GO:0001717	Process	Conversion of seryl-tRNAsec to selenocys-tRNAsec	IEA
GO:0003723	Function	RNA binding	IEA
GO:0005515	Function	Protein binding	IPI	22190034, 32296183
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	ISS
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	ISS
GO:0005829	Component	Cytosol	TAS
GO:0006412	Process	Translation	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0098621	Function	O-phosphoseryl-tRNA(Sec) selenium transferase activity	IEA

MIM	HGNC	e!Ensembl
613009	30605	ENSG00000109618

Protein

UniProt ID

Q9HD40

Protein name

O-phosphoseryl-tRNA(Sec) selenium transferase (EC 2.9.1.2) (Liver-pancreas antigen) (LP) (SLA-p35) (SLA/LP autoantigen) (Selenocysteine synthase) (Sec synthase) (Selenocysteinyl-tRNA(Sec) synthase) (Sep-tRNA:Sec-tRNA synthase) (SepSecS) (Soluble liver ant

Protein function

Converts O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis.

PDB

3HL2 , 4ZDL , 4ZDO , 4ZDP , 7L1T , 7MDL , 8G9Z

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF05889	SepSecS	61 → 459	O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS	Domain

Tissue specificity

TISSUE SPECIFICITY: Primarily expressed in liver, pancreas, kidney and lung. Overexpressed in PHA-stimulated T-cells.

Sequence

MNRESFAAGERLVSPAYVRQGCEARRSHEHLIRLLLEKGKCPENGWDESTLELFLHELAI
MDSNNFLGNCGVGEREGRVASALVARRHYRFIHGIGRSGDISAVQPKAAGSSLLNKITNS
LVLDIIKLAGVHTVANCFVVPMATGMSLTLCFLTLRHKRPKAKYIIWPRIDQKSCFKSMI
TAGFEPVVIENVLEGDELRTDLKAVEAKVQELGPDCILCIHSTTSCFAPRVPDRLEELAV
ICANYDIPHIVNNAYGVQSSKCMHLIQQGARVGRIDAFVQSLDKNFMVPVGGAIIAGFND
SFIQEISKMYPGRASASPSLDVLITLLSLGSNGYKKLLKERKEMFSYLSNQIKKLSEAYN
ERLLHTPHNPISLAMTLKTLDEHRDKAVTQLGSMLFTRQVSGARVVPLGSMQTVSGYTFR
GFMSHTNNYPCAYLNAASAIGMKMQDVDLFIKRLDRCLKAVRKERSKESDDNYDKTEDVD
IEEMALKLDNVLLDTYQDASS

Sequence length

501

Interactions

View interactions

	KEGG		Reactome
	Selenocompound metabolism Aminoacyl-tRNA biosynthesis Metabolic pathways		Selenocysteine synthesis

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Pontoneocerebellar hypoplasia	Pontocerebellar hypoplasia type 2D, pontoneocerebellar hypoplasia	rs267607036, rs267607035, rs776969714, rs1057518887, rs1309003036, rs1712612585	N/A

Show/Hide Unknown Diseases (3)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Metabolic Syndrome	Metabolic syndrome	N/A	N/A	GWAS
Progressive Cerebello-Cerebral Atrophy	progressive cerebello-cerebral atrophy	N/A	N/A	GenCC
Spastic Ataxia	spastic ataxia	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (24)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Adenocarcinoma of Lung	Associate	36879187
Ataxia	Associate	27576344
Atrial Fibrillation	Associate	36952494
Atrophy	Associate	32295391, 35091508
Brain Diseases	Associate	26115735, 28133863, 35091508
Cerebellar Ataxia	Associate	29464431
Cerebellar Diseases	Associate	29464431
Chromosome Aberrations	Associate	20920667
Cognition Disorders	Associate	29464431
Crohn Disease	Associate	23112913
Fractures Spontaneous	Associate	27576344
Glioblastoma	Associate	17002787
Hepatitis Autoimmune	Associate	10931155, 17006990
Huntington Disease	Associate	37761892
Immunologic Deficiency Syndromes	Associate	32295391
Mental Disorders	Associate	27576344
Microcephaly	Associate	29464431, 35091508
Muscle Spasticity	Associate	27576344
Neurodegenerative Diseases	Associate	35091508
Neurologic Manifestations	Associate	27576344
Pontocerebellar Hypoplasia	Associate	29464431
Seizures	Associate	27576344
Stroke	Associate	36952494
Syndrome	Associate	28133863

SEPSECS (Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase)