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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 14 days ago
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SEPSECS
Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase
Chromosome 4 Β· 4p15.2
NCBI Gene: 51091Ensembl: ENSG00000109618.13HGNC: HGNC:30605UniProt: A0A7P0TA23
48PubMed Papers
21Diseases
0Drugs
105Pathogenic Variants
RESEARCH IMPACT
Variant-Rich
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
cytoplasmprotein bindingcytosolO-phosphoseryl-tRNA(Sec) selenium transferase activitypontocerebellar hypoplasia type 2Dpontocerebellar hypoplasianeurodegenerative diseaseNon-syndromic pontocerebellar hypoplasia
✦AI Summary

SEPSECS encodes O-phosphoseryl-tRNA:selenocysteine-tRNA synthase, an enzyme that catalyzes the terminal step of selenocysteine biosynthesis by converting O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) 1. This reaction is essential for the incorporation of selenocysteine, the 21st genetically encoded amino acid, into selenoproteins 1. The enzyme functions as a tetramer with four active sites but binds only two tRNA molecules due to structural constraints imposed by its C-terminal α-helical extension, which evolved specifically in vertebrates to optimize tRNA binding and prevent complex aggregation 23. Structurally, tRNA binding induces conformational changes that organize the active sites through electrostatic interactions between the tRNA's acceptor, TΨC, and variable arms with specific helices of SEPSECS 3. Disease-wise, SEPSECS mutations cause Pontocerebellar Hypoplasia Type 2D (PCH2D), a rare neurological disorder characterized by progressive cerebellar atrophy, microcephaly, intellectual disability, and motor dysfunction 45. The protein also serves as an autoantigen (SLA/LP) in autoimmune hepatitis, where anti-SEPSECS antibodies are associated with more severe disease phenotypes 16.

Sources cited
1
SEPSECS catalyzes the conversion of O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) and is known as SLA/LP autoantigen
PMID: 20623998
2
Human SEPSECS binds only two tRNA molecules despite having four active sites due to C-terminal Ξ±-helical extension
PMID: 39385655
3
tRNA binding induces conformational changes and is mediated by electrostatic interactions
PMID: 36929010
4
SEPSECS mutations cause Pontocerebellar Hypoplasia Type 2D with specific neurological symptoms
PMID: 41070650
5
PCH2D is characterized by cerebellar atrophy, microcephaly, and motor dysfunction
PMID: 36085396
6
Anti-SEPSECS antibodies in autoimmune hepatitis are associated with severe phenotypes
PMID: 39817450
Disease Associationsβ“˜21
pontocerebellar hypoplasia type 2DOpen Targets
0.76Strong
pontocerebellar hypoplasiaOpen Targets
0.66Moderate
neurodegenerative diseaseOpen Targets
0.54Moderate
Non-syndromic pontocerebellar hypoplasiaOpen Targets
0.51Moderate
genetic disorderOpen Targets
0.50Moderate
pontocerebellar hypoplasia type 2Open Targets
0.37Weak
progressive cerebello-cerebral atrophyOpen Targets
0.37Weak
spastic ataxiaOpen Targets
0.34Weak
lymphatic system diseaseOpen Targets
0.29Weak
acute tonsillitisOpen Targets
0.28Weak
arthrogryposis multiplex congenitaOpen Targets
0.27Weak
Cerebral hypoplasiaOpen Targets
0.27Weak
isolated cerebellar hypoplasia/agenesisOpen Targets
0.27Weak
KyphosisOpen Targets
0.27Weak
SeizureOpen Targets
0.27Weak
Severe global developmental delayOpen Targets
0.27Weak
Spinal rigidityOpen Targets
0.27Weak
cerebellar ataxiaOpen Targets
0.26Weak
DysarthriaOpen Targets
0.26Weak
NeurodegenerationOpen Targets
0.26Weak
Pontocerebellar hypoplasia 2DUniProt
Pathogenic Variants105
NM_016955.5(SEPSECS):c.808dupPathogenic
not provided|Pontocerebellar hypoplasia type 2D|Inborn genetic diseases|Pontoneocerebellar hypoplasia
β˜…β˜…β˜†β˜†2026
NM_016955.4(SEPSECS):c.811C>T (p.Arg271Ter)Pathogenic
not provided|Inborn genetic diseases|Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2026β†’ Residue 271
NM_016955.4(SEPSECS):c.835del (p.Val279fs)Pathogenic
not provided|Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2026β†’ Residue 279
NM_016955.4(SEPSECS):c.114+3A>GPathogenic
Neurodevelopmental abnormality|not provided|Pontoneocerebellar hypoplasia|Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2026
NM_016955.4(SEPSECS):c.715G>A (p.Ala239Thr)Pathogenic
Pontocerebellar hypoplasia type 2D|not provided|Pontoneocerebellar hypoplasia
β˜…β˜…β˜†β˜†2025β†’ Residue 239
NM_016955.4(SEPSECS):c.41C>A (p.Ser14Ter)Pathogenic
not provided|Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2025β†’ Residue 14
NM_016955.4(SEPSECS):c.194A>G (p.Asn65Ser)Likely pathogenic
Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2025β†’ Residue 65
NM_016955.4(SEPSECS):c.289C>T (p.Arg97Ter)Pathogenic
not provided|Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2025β†’ Residue 97
NM_016955.4(SEPSECS):c.919del (p.Ser307fs)Pathogenic
not provided|Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2025β†’ Residue 307
NM_016955.4(SEPSECS):c.1148dup (p.His383fs)Pathogenic
not provided|Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2025β†’ Residue 383
NM_016955.4(SEPSECS):c.163_164del (p.Leu55fs)Pathogenic
not provided|Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2025β†’ Residue 55
NM_016955.4(SEPSECS):c.1027-2A>GLikely pathogenic
Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2025
NM_016955.4(SEPSECS):c.466C>T (p.Arg156Ter)Pathogenic
not provided|Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2025β†’ Residue 156
NM_016955.4(SEPSECS):c.612dup (p.Val205fs)Pathogenic
Inborn genetic diseases|not provided|Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2025β†’ Residue 205
NM_016955.4(SEPSECS):c.1178C>A (p.Ser393Ter)Pathogenic
not provided|Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2025β†’ Residue 393
NM_016955.4(SEPSECS):c.448_449del (p.Leu150fs)Pathogenic
not provided|Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2025β†’ Residue 150
NM_016955.4(SEPSECS):c.389-13_404delLikely pathogenic
not provided|Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2025
NM_016955.4(SEPSECS):c.1169_1173del (p.Gln390fs)Pathogenic
not provided|Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2024β†’ Residue 390
NM_016955.4(SEPSECS):c.482del (p.Lys161fs)Pathogenic
not provided|Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2024β†’ Residue 161
NM_016955.4(SEPSECS):c.313C>T (p.Gln105Ter)Pathogenic
not provided|Pontocerebellar hypoplasia type 2D
β˜…β˜…β˜†β˜†2024β†’ Residue 105
View on ClinVar β†—
Related Genes
SECISBP2LShared pathway100%EEFSECShared pathway100%SECISBP2Protein interaction100%PSTKProtein interaction99%SCLYProtein interaction98%TRNAU1APProtein interaction95%
Tissue Expression6 tissues
Liver
100%
Bone Marrow
60%
Ovary
30%
Lung
22%
Heart
21%
Brain
16%
Gene Interaction Network
Click a node to explore
SEPSECSSECISBP2LEEFSECSECISBP2PSTKSCLYTRNAU1AP
PROTEIN STRUCTURE
Preparing viewer…
PDB8G9Z Β· 2.07 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
1.10LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.81 [0.61–1.10]
RankingsWhere SEPSECS stands among ~20K protein-coding genes
  • #9,128of 20,598
    Most Researched48
  • #742of 5,498
    Most Pathogenic Variants105 Β· top quartile
  • #11,176of 17,882
    Most Constrained (LOEUF)1.10
Genes detectedSEPSECS
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Human SepSecS or SLA/LP: selenocysteine formation and autoimmune hepatitis.
PMID: 20623998
Biol Chem Β· 2010
1.00
2
Clonal analysis of SepSecS-specific B and T cells in autoimmune hepatitis.
PMID: 39817450
J Clin Invest Β· 2025
0.90
3
[Pontocerebellar hypoplasia type 2D caused by compound heterozygous variants in the SEPSECS gene: A case report and literature review].
PMID: 41070650
Zhonghua Yi Xue Yi Chuan Xue Za Zhi Β· 2025
0.80
4
A susceptibility gene signature for ERBB2-driven mammary tumour development and metastasis in collaborative cross mice.
PMID: 39067134
EBioMedicine Β· 2024
0.70
5
Analysis of the Clinical Features and Imaging Findings of Pontocerebellar Hypoplasia Type 2D Caused by Mutations in SEPSECS Gene.
PMID: 36085396
Cerebellum Β· 2023
0.60