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EEFSEC

gene
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Also known as SELBEFSEC

Summary

EEFSEC (eukaryotic elongation factor, selenocysteine-tRNA specific, HGNC:24614) is a protein-coding gene on chromosome 3q21.3, encoding Selenocysteine-specific elongation factor (P57772). Translation factor required for the incorporation of the rare amino acid selenocysteine encoded by UGA codons. It is a selective cancer dependency (DepMap: 48.8% of cell lines).

Enables GTPase activity. Involved in selenocysteine incorporation. Predicted to be located in cytoplasm and nucleus. Predicted to be part of ribonucleoprotein complex.

Source: NCBI Gene 60678 — automated summary from GO annotations (Alliance of Genome Resources).

At a glance

  • Gene–disease (curated): neurodevelopmental disorder (Strong, GenCC) — +1 more curated relationship
  • GWAS associations: 139 (top 1% of genes corpus-wide)
  • Clinical variants (ClinVar): 131 total — 2 pathogenic, 3 likely-pathogenic
  • GTEx eGene: eQTL in 38 tissues, sQTL in 2 (q < 0.05)
  • Phenotypes (HPO): 80
  • Cancer dependency (DepMap): dependent in 48.8% of screened cell lines
  • Constraint (gnomAD): pLI 0.00 (LoF-tolerant), LOEUF 1.34 (unconstrained)
  • MANE Select transcript: NM_021937

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24614
Approved symbolEEFSEC
Nameeukaryotic elongation factor, selenocysteine-tRNA specific
Location3q21.3
Locus typegene with protein product
StatusApproved
AliasesSELB, EFSEC
Ensembl geneENSG00000132394
Ensembl biotypeprotein_coding
OMIM607695
Entrez60678

Gene structure

Transcript identifiers

Ensembl transcripts: 21 — 16 protein_coding, 3 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined

MANE Select: ENST00000254730

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 3: 1, TSL 5: 2

ENST00000254730, ENST00000483457, ENST00000483569, ENST00000484438, ENST00000868106, ENST00000868107, ENST00000868108, ENST00000868109, ENST00000934138, ENST00000945661, ENST00000998545, ENST00000998546, ENST00001038391, ENST00001038392, ENST00001110385, ENST00001122113, ENST00001122114, ENST00001122115, ENST00001122116, ENST00001122117, ENST00001142888

RefSeq mRNA: 8 — MANE Select: NM_021937 NM_001437809, NM_001437810, NM_001437811, NM_001437812, NM_001437813, NM_001437814, NM_001437815, NM_021937

CCDS: CCDS33849

Canonical transcript exons

ENST00000254730 — 7 exons

ExonStartEnd
ENSE00000903888128153481128153823
ENSE00000903893128358217128358373
ENSE00001047553128262128128262224
ENSE00001177853128341233128341889
ENSE00001313311128264617128264781
ENSE00003573560128408069128408646
ENSE00003628405128246836128247043

Expression profiles

Bgee: expression breadth ubiquitous, 135 present calls, max score 89.30.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.9112 / max 107.6742, expressed in 1762 samples.

Highest expression (Bgee): apex of heart, heart left ventricle, gastrocnemius, hindlimb stylopod muscle, muscle of leg.

Genetic regulation across tissues (GTEx eQTL / sQTL)

EEFSEC is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 38 tissues and its splicing (sQTL) in 2 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

showing 20 of 40 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Nerve Tibialeqtl1.2e-20-0.263:128146667:A:G
Testissqtl3.0e-19-0.773:128319530:C:A
Testiseqtl1.6e-18+0.373:128011923:T:C
Brain Frontal Cortex BA9eqtl6.8e-16+0.393:128137730:T:A
Skin Sun Exposed Lower legeqtl1.1e-14+0.243:128244348:G:C
Heart Left Ventricleeqtl2.2e-14+0.293:128089659:C:G
Muscle Skeletaleqtl2.9e-14-0.283:128185123:GTT:G
Adipose Subcutaneouseqtl5.9e-14+0.233:128137730:T:A
Esophagus Musculariseqtl2.0e-13-0.283:128146667:A:G
Whole Bloodeqtl2.9e-12+0.123:128098665:C:T
Artery Tibialsqtl3.5e-12+0.703:128168114:G:A
Heart Atrial Appendageeqtl2.0e-11+0.273:128100219:G:C
Skin Not Sun Exposed Suprapubiceqtl5.5e-11-0.253:128097590:T:C
Thyroideqtl2.6e-10-0.303:128153759:A:G
Brain Anterior cingulate cortex BA24eqtl1.2e-09-0.403:128173194:T:C
Brain Cortexeqtl7.0e-09+0.363:128137730:T:A
Artery Tibialeqtl2.4e-08-0.183:128162770:G:A
Brain Spinal cord cervical c-1eqtl3.8e-08-0.483:128146667:A:G
Cells Cultured fibroblastseqtl1.5e-07+0.183:128089972:A:G
Esophagus Mucosaeqtl1.9e-07-0.263:128128832:C:T

FANTOM5 promoters

1 alternative TSS:

Promoter IDTPM avgSamples expressed
384368.91121762

Top tissues by expression

showing 100 of 135 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
apex of heartUBERON:000209889.30gold quality
heart left ventricleUBERON:000208488.25gold quality
gastrocnemiusUBERON:000138887.40gold quality
hindlimb stylopod muscleUBERON:000425286.75gold quality
muscle of legUBERON:000138386.60gold quality
granulocyteCL:000009485.97gold quality
heartUBERON:000094885.54gold quality
right lobe of liverUBERON:000111485.52gold quality
skeletal muscle tissueUBERON:000113484.36gold quality
left uterine tubeUBERON:000130384.36gold quality
right atrium auricular regionUBERON:000663183.96gold quality
popliteal arteryUBERON:000225083.84gold quality
tibial arteryUBERON:000761083.82gold quality
skin of legUBERON:000151183.65gold quality
body of uterusUBERON:000985383.47gold quality
right testisUBERON:000453483.46gold quality
left testisUBERON:000453383.25gold quality
zone of skinUBERON:000001483.23gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099183.21gold quality
adult mammalian kidneyUBERON:000008283.21gold quality
testisUBERON:000047383.06gold quality
ectocervixUBERON:001224983.00gold quality
tibial nerveUBERON:000132382.95gold quality
cortical plateUBERON:000534382.93gold quality
skin of abdomenUBERON:000141682.88gold quality
ganglionic eminenceUBERON:000402382.81gold quality
left coronary arteryUBERON:000162682.73gold quality
liverUBERON:000210782.70gold quality
muscle tissueUBERON:000238582.67gold quality
ascending aortaUBERON:000149682.46gold quality
endocervixUBERON:000045882.44gold quality
thoracic aortaUBERON:000151582.43gold quality
myometriumUBERON:000129682.39gold quality
right coronary arteryUBERON:000162582.37gold quality
subcutaneous adipose tissueUBERON:000219082.21gold quality
right ovaryUBERON:000211882.20gold quality
mucosa of transverse colonUBERON:000499182.05gold quality
lower esophagus muscularis layerUBERON:003583381.88gold quality
lower esophagusUBERON:001347381.86gold quality
esophagogastric junction muscularis propriaUBERON:003584181.84gold quality
placentaUBERON:000198781.78gold quality
prefrontal cortexUBERON:000045181.69gold quality
bloodUBERON:000017881.47gold quality
spleenUBERON:000210681.41gold quality
descending thoracic aortaUBERON:000234581.35gold quality
cortex of kidneyUBERON:000122581.23gold quality
ventricular zoneUBERON:000305381.21gold quality
left ovaryUBERON:000211981.19gold quality
adipose tissueUBERON:000101381.16gold quality
leukocyteCL:000073881.12gold quality
esophagusUBERON:000104381.08gold quality
vaginaUBERON:000099681.01gold quality
kidneyUBERON:000211381.00gold quality
ovaryUBERON:000099280.96gold quality
muscle layer of sigmoid colonUBERON:003580580.95gold quality
fundus of stomachUBERON:000116080.91gold quality
body of stomachUBERON:000116180.90gold quality
fallopian tubeUBERON:000388980.85gold quality
uterine cervixUBERON:000000280.83gold quality
monocyteCL:000057680.82gold quality
anatomical systemUBERON:000046780.82gold quality
multicellular organismUBERON:000046880.82gold quality
esophagus mucosaUBERON:000246980.74gold quality
thoracic mammary glandUBERON:000520080.64gold quality
frontal cortexUBERON:000187080.52gold quality
prostate glandUBERON:000236780.45gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047380.18gold quality
stromal cell of endometriumCL:000225580.15gold quality
right lungUBERON:000216780.06gold quality
right lobe of thyroid glandUBERON:000111979.96gold quality
omental fat padUBERON:001041479.95gold quality
right hemisphere of cerebellumUBERON:001489079.89gold quality
upper lobe of left lungUBERON:000895279.76gold quality
metanephros cortexUBERON:001053379.59gold quality
lower esophagus mucosaUBERON:003583479.46gold quality
lymph nodeUBERON:000002979.45gold quality
body of pancreasUBERON:000115079.45gold quality
cerebellumUBERON:000203779.42gold quality
stomachUBERON:000094579.39gold quality
cerebellar cortexUBERON:000212979.36gold quality
cerebellar hemisphereUBERON:000224579.34gold quality
transverse colonUBERON:000115779.31gold quality
colonUBERON:000115579.30gold quality
small intestine Peyer’s patchUBERON:000345479.25gold quality
right adrenal glandUBERON:000123379.24gold quality
right uterine tubeUBERON:000130279.12gold quality
right frontal lobeUBERON:000281079.10gold quality
cerebral cortexUBERON:000095679.03gold quality
urinary bladderUBERON:000125578.98gold quality
smooth muscle tissueUBERON:000113578.88gold quality
left lobe of thyroid glandUBERON:000112078.76gold quality
small intestineUBERON:000210878.72gold quality
intestineUBERON:000016078.70gold quality
left adrenal glandUBERON:000123478.65gold quality
hypothalamusUBERON:000189878.58gold quality
minor salivary glandUBERON:000183078.57gold quality
saliva-secreting glandUBERON:000104478.55gold quality
mucosa of stomachUBERON:000119978.53gold quality
bone marrowUBERON:000237178.51gold quality
Brodmann (1909) area 9UBERON:001354078.51gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no2.59

HPA expression

RNA tissue specificity: Low tissue specificity

showing 60 of 75 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Cerebellumtissue13.0not detected
Caudate putamentissue12.9
Frontal cortextissue12.3
Vaginatissue11.7low
Hippocampal formationtissue11.4
Hypothalamustissue10.5
Substantia nigratissue10.5
Basal gangliatissue10.4not detected
Septumtissue10.4
Cerebral cortextissue10.3low
Somatosensory cortextissue10.3
Midbraintissue10.2
Olfactory bulbtissue10.1
Motor cortextissue10.0
Amygdalatissue10.0
Ventral forebraintissue10.0
Ponstissue9.9
Entorhinal cortextissue9.8
Prefrontal cortextissue9.7
Putamentissue9.7
Spinal cordtissue9.7
Retrosplenial cortextissue9.7
Medulla oblongatatissue9.6
Thalamustissue9.6
Insular cortextissue9.6
Superior colliculitissue9.5
Retrosplenial and cingulate cortextissue9.5
Periaqueductal graytissue9.4
Temporal cortextissue9.2
Corpus callosumtissue9.1
Occipital cortextissue8.8
Pituitary glandtissue8.6
Skeletal muscletissue4.5not detected
Heart muscletissue3.2not detected
Skin 1tissue3.1low
Small intestinetissue3.0low
Parathyroid glandtissue2.8not detected
Lymph nodetissue2.1not detected
Cervixtissue2.0not detected
Livertissue1.9low
Seminal vesicletissue1.8low
Salivary glandtissue1.8low
Kidneytissue1.6medium
Placentatissue1.5medium
Fallopian tubetissue1.5low
Colontissue1.4low
Pancreastissue1.4medium
Prostatetissue1.4not detected
Ovarytissue1.3medium
Thyroid glandtissue1.3medium
Testistissue1.2low
Esophagustissue1.2medium
Adipose tissuetissue1.1not detected
Tonsiltissue1.1medium
Nucleus accumbenstissue1.0
Locus coeruleustissue1.0
Hippocampustissue1.0not detected
Postcentral gyrustissue1.0
Choroid plexustissue0.9
Spleentissue0.9not detected

Brain sub-regions (HPA Brain Atlas): detected in 191; highest nTPM — Blood vessel (13.9), Ventral hippocampus (11.4), Subiculum (10.6), Dorsal hippocampus (10.5), Dorsal spinal cord (9.7).

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ZNF143

miRNA regulators (miRDB)

Targeting EEFSEC by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific).

showing 30 of 38 miRNAs:

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-6870-5P99.9968.552115
HSA-MIR-4723-5P99.9768.702034
HSA-MIR-569899.9768.492029
HSA-MIR-7111-5P99.9768.482062
HSA-MIR-185-3P99.9567.011743
HSA-MIR-449299.8768.253611
HSA-MIR-3065-3P99.8770.251407
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-472999.6972.184233
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-10394-5P99.6566.831852
HSA-MIR-120599.6566.761826
HSA-MIR-76299.5866.611994
HSA-MIR-486-3P99.5166.821901
HSA-MIR-449899.4767.422360
HSA-MIR-127599.4767.902749
HSA-MIR-6722-3P99.4567.621919
HSA-MIR-6731-5P99.2867.422375
HSA-MIR-808599.2867.562362
HSA-MIR-450599.2767.812678
HSA-MIR-578799.2267.862628
HSA-MIR-6852-5P99.1766.692073
HSA-MIR-5001-5P99.0566.761972
HSA-MIR-1909-3P99.0366.561662
HSA-MIR-6829-5P98.8665.121480
HSA-MIR-6846-5P98.8165.861121
HSA-MIR-6848-5P98.8165.491126
HSA-MIR-465698.7966.221306
HSA-MIR-38498.7167.341229
HSA-MIR-446398.5666.051071

Functional genomics

gnomAD constraint: pLI 9.56e-16, LOEUF 1.34, missense Z 0.58 — population loss-of-function intolerance (pLI ≥ 0.9 = LoF-intolerant; lower LOEUF = more constrained). gnomAD

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000254730 — one region, missense o/e 0.93. DepMap (CRISPR cell-line fitness): dependent in 48.8% of screened cell lines.

Most-dependent cell lines (DepMap gene-effect, lower = stronger; ≤ −0.5 shown): TC-71 (-3.205), MHH-ES-1 (-2.578), SU-DHL-8 (-2.265), OCI-LY-19 (-2.205), SU-DHL-5 (-2.118), 8-MG-BA (-2.05), SF126 (-1.933), OCI-AML2 (-1.79), SK-N-DZ (-1.724), BICR 10 (-1.643), SU-DHL-10 (-1.555), Y-79 (-1.498), OPM-2 (-1.497), L-428 (-1.457), JHOS-4 (-1.431).

Literature-anchored findings (GeneRIF, showing 6)

  • SECIS binding induces a conformational change in SBP2 that recruits eEFSec, which in concert with the Sec incorporation domain gains access to the ribosomal A site (PMID:18948268)
  • eEFSec employs a non-canonical mechanism involving the distinct C-terminal domain 4 for the release of the selenocysteinyl-tRNA during decoding on the ribosome (PMID:27708257)
  • EEFSEC, which encodes selenocysteine-tRNA specific eukaryotic elongation factor, participates in the incorporation of selenocysteine into selenoproteins. Selenoproteins serve critical cellular homeostatic functions in maintaining redox status and antioxidant defenses, as well as modulating inflammatory responses. These physiologic functions have been linked to the parturition process and preterm birth. (PMID:28877031)
  • In this genomewide association study, we found that variants at the EBF1, EEFSEC, AGTR2, WNT4, ADCY5, and RAP2C loci were associated with gestational duration and variants at the EBF1, EEFSEC, and AGTR2 loci with preterm birth. (PMID:28877031)
  • [EEFSEC knockdown inhibits proliferation, migration and invasion of prostate cancer cells in vitro]. (PMID:35012909)
  • Association of rs142548867 (EEFSEC) and periodontitis Grade C in a young Brazilian population. (PMID:37466550)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioeefsecENSDARG00000004696
mus_musculusEefsecENSMUSG00000033216
rattus_norvegicusEefsecENSRNOG00000012954
drosophila_melanogastereEFSecFBGN0034627
caenorhabditis_elegansefsc-1WBGENE00008133

Paralogs (18): MTIF2 (ENSG00000085760), GTPBP1 (ENSG00000100226), EEF1A2 (ENSG00000101210), GSPT1 (ENSG00000103342), EFTUD2 (ENSG00000108883), HBS1L (ENSG00000112339), EIF2S3 (ENSG00000130741), EFL1 (ENSG00000140598), GUF1 (ENSG00000151806), EEF1A1 (ENSG00000156508), EIF5B (ENSG00000158417), GFM2 (ENSG00000164347), EEF2 (ENSG00000167658), GFM1 (ENSG00000168827), GTPBP2 (ENSG00000172432), TUFM (ENSG00000178952), EIF2S3B (ENSG00000180574), GSPT2 (ENSG00000189369)

Mouse-model phenotypes

Observed phenotypes of the mouse ortholog (MGI:2137092) from MGI (Alliance of Genome Resources) — knockout/mutant phenotypes, ranked by annotation count. 2 distinct phenotype terms.

Mouse phenotype (MP)Records
impaired righting response1
preweaning lethality, complete penetrance1

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

OrganismUniProtIdentityMethod
Halorubrum lacusprofundi ATCC 49239B9LSM677.1%Diamond
Methanocaldococcus jannaschii DSM 2661Q5791839.1%Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
SEC61A1protein-coding29927
RUVBL1protein-coding8607
RUVBL1-AS1ncRNA100874089
DNAJB8protein-coding165721
DNAJB8-AS1ncRNA285224
GATA2-AS1ncRNA101927167
GATA2protein-coding2624
KBTBD12protein-coding166348

Protein

Protein identifiers

Selenocysteine-specific elongation factor — P57772 (reviewed: P57772)

Alternative names: Elongation factor sec, Eukaryotic elongation factor, selenocysteine-tRNA-specific

All UniProt accessions (2): C9J8T0, P57772

UniProt curated annotations — full annotation on UniProt →

Function. Translation factor required for the incorporation of the rare amino acid selenocysteine encoded by UGA codons. Replaces the eRF1-eRF3-GTP ternary complex for the insertion of selenocysteine directed by the UGA codon. Insertion of selenocysteine at UGA codons is mediated by SECISBP2 and EEFSEC: SECISBP2 (1) specifically binds the SECIS sequence once the 80S ribosome encounters an in-frame UGA codon and (2) contacts the RPS27A/eS31 of the 40S ribosome before ribosome stalling. (3) GTP-bound EEFSEC then delivers selenocysteinyl-tRNA(Sec) to the 80S ribosome and adopts a preaccommodated state conformation. (4) After GTP hydrolysis, EEFSEC dissociates from the assembly, selenocysteinyl-tRNA(Sec) accommodates, and peptide bond synthesis and selenoprotein elongation occur.

Subcellular location. Cytoplasm. Nucleus.

Disease relevance. Neurodevelopmental disorder with progressive spasticity and brain abnormalities (NEDPSB) [MIM:621102] An autosomal recessive disorder with onset in infancy or early childhood, and characterized by global developmental delay with intellectual disability, poor or absent speech, progressive spasticity, ataxia, and seizures. Brain imaging primarily shows cerebral and/or cerebellar hypoplasia with delayed myelination, and progressive cerebellar atrophy in about half of patients. The disease is caused by variants affecting the gene represented in this entry.

Similarity. Belongs to the TRAFAC class translation factor GTPase superfamily. Classic translation factor GTPase family. SelB subfamily.

Isoforms (2)

UniProt IDNamesCanonical?
P57772-11yes
P57772-22

RefSeq proteins (8): NP_001424738, NP_001424739, NP_001424740, NP_001424741, NP_001424742, NP_001424743, NP_001424744, NP_068756* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000795T_Tr_GTP-bd_domDomain
IPR004161EFTu-like_2Domain
IPR009000Transl_B-barrel_sfHomologous_superfamily
IPR027417P-loop_NTPaseHomologous_superfamily
IPR049393eEFSec_IIIDomain
IPR049394eEFSec_CDomain
IPR050055EF-Tu_GTPaseFamily

Pfam: PF00009, PF03144, PF21131, PF21208

Catalyzed reactions (Rhea)

  • GTP + H2O = GDP + phosphate + H(+) (RHEA:19669)

UniProt features (98 total): strand 39, helix 15, binding site 13, region of interest 6, sequence variant 6, mutagenesis site 6, turn 4, modified residue 3, chain 1, domain 1, splice variant 1, sequence conflict 1, short sequence motif 1, compositionally biased region 1

Structure

Experimental structures (PDB)

4 structures by resolution:

PDBTitleMethodResolution (Å)
5IZLThe crystal structure of human eEFSec in complex with GDPCPX-RAY DIFFRACTION2.72
7ZJWRabbit 80S ribosome as it decodes the Sec-UGA codonELECTRON MICROSCOPY2.8
5IZKThe crystal structure of human eEFSec in complex with GDPX-RAY DIFFRACTION3.25
5IZMThe crystal structure of human eEFSec in complex with GDPNPX-RAY DIFFRACTION3.4

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P57772-F179.980.28

Human Protein Atlas

Protein class: Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): nuclear bodies; nucleoplasm; cytosol

Antibody reliability (HPA): IH approved · IF approved

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (13)

PositionRole
19GDP
19GTP
21GDP
21GTP
21Mg(2+)
22GDP
22GTP
48Mg(2+)
92Mg(2+)
149GDP
149GTP
187GDP
187GTP

Post-translational modifications (3)

TypePositions
Phosphoserine537
Phosphothreonine545
Omega-n-methylarginine556

Mutagenesis-validated functional residues (6)

PositionPhenotype
96abolished gtpase activity.
229abolished ability to mediate insertion of selenocysteine.
230abolished ability to mediate insertion of selenocysteine.
285abolished ability to mediate insertion of selenocysteine.
583–584does not affect ability to mediate insertion of selenocysteine.

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 4; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

4 pathways:

IDPathwayEvidence
R-HSA-1430728Metabolism—
R-HSA-71291Metabolism of amino acids and derivatives—
R-HSA-2408522Selenoamino acid metabolism—
R-HSA-2408557Selenocysteine synthesiselectronic

MSigDB gene sets: 269 (showing top): GOBP_TRANSLATION, GOBP_POST_TRANSCRIPTIONAL_REGULATION_OF_GENE_EXPRESSION, GOBP_TRANSLATIONAL_ELONGATION, chr3q21, GOBP_REGULATION_OF_TRANSLATION, GOCC_RIBONUCLEOPROTEIN_COMPLEX, SCGGAAGY_ELK1_02, GOMF_GTPASE_ACTIVITY, GOMF_MRNA_BINDING, GOMF_TRNA_BINDING, GOMF_TRANSLATION_ELONGATION_FACTOR_ACTIVITY, GOMF_HYDROLASE_ACTIVITY_ACTING_ON_ACID_ANHYDRIDES, GOMF_RIBONUCLEOPROTEIN_COMPLEX_BINDING, HSF2_01, GOBP_REGULATION_OF_PROTEIN_METABOLIC_PROCESS

GO Biological Process (2): selenocysteine incorporation (GO:0001514), translation (GO:0006412)

GO Molecular Function (8): tRNA binding (GO:0000049), translation elongation factor activity (GO:0003746), GTPase activity (GO:0003924), GTP binding (GO:0005525), selenocysteine insertion sequence binding (GO:0035368), ribonucleoprotein complex binding (GO:0043021), nucleotide binding (GO:0000166), hydrolase activity (GO:0016787)

GO Cellular Component (3): nucleus (GO:0005634), cytoplasm (GO:0005737), ribonucleoprotein complex (GO:1990904)

Reactome top-level categories

3 top-level categories:

CategoryPathways
Selenoamino acid metabolism1
Metabolism of amino acids and derivatives1
Metabolism1

GO top-level categories

23 GO namespaces:

CategoryTerms
translational elongation2
translational readthrough1
peptidyltransferase activity1
translational initiation1
translational termination1
macromolecule biosynthetic process1
protein metabolic process1
protein biosynthetic process1
RNA binding1
translation factor activity1
ribonucleoside triphosphate phosphatase activity1
guanyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
anion binding1
mRNA binding1
protein-containing complex binding1
nucleoside phosphate binding1
heterocyclic compound binding1
catalytic activity1
intracellular membrane-bounded organelle1
intracellular anatomical structure1
cellular anatomical structure1
protein-containing complex1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 2 of 13 annotations. The rest are phylogenetic / computational / electronic (IEA).

2 experimentally-supported GO terms:

GO termNSEvidence
selenocysteine incorporationBPdirect assay
GTPase activityMFdirect assay

Protein interactions and networks

STRING

showing 15 of 1,247 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
EEFSECSECISBP2Q96T21994
EEFSECPSTKQ8IV42988
EEFSECSEPHS1P49903858
EEFSECSEPSECSQ9HD40852
EEFSECTRNAU1APQ9NX07827
EEFSECSARS1P49591824
EEFSECSEPHS2Q99611824
EEFSECSARS2Q9NP81813
EEFSECM0R2C6M0R2C6812
EEFSECSELENOSQ9BQE4717
EEFSECSELENOTP62341713
EEFSECSELENONQ9NZV5692
EEFSECSELENOFO60613686
EEFSECSCLYQ96I15683
EEFSECSELENOOQ9BVL4681

IntAct

Human interaction partners of EEFSEC in IntAct, one row per partner (best MIscore; records = supporting IntAct interaction records).

2 partners by confidence:

PartnerInteraction typeMIscoreRecords
HSPA8association0.3501
SOX17association0.3501

BioGRID (69 interactions; top human partners by supporting records): KRAS (Synthetic Lethality; 2 records), NUDT21 (Affinity Capture-RNA; 2 records), ANKRD11 (Affinity Capture-MS), ATG16L1 (Affinity Capture-MS), BCAT1 (Co-fractionation), CAMSAP1 (Cross-Linking-MS (XL-MS)), CD6 (Affinity Capture-MS), CEBPA (Protein-peptide), CLUH (Co-fractionation), DDRGK1 (Affinity Capture-MS), DDX39A (Affinity Capture-RNA), DYNLT1 (Co-fractionation), EFTUD2 (Co-fractionation), EGFR (Negative Genetic), ENG (Affinity Capture-MS)

Disease & clinical

Genetic variants

Variant evidence for EEFSEC: 131 ClinVar records (5 pathogenic / likely pathogenic); 139 GWAS associations. Per-variant detail is on Sugi Variant.

ClinVar

131 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic2
Likely pathogenic3
Uncertain significance104
Likely benign7
Benign4

Top pathogenic / likely-pathogenic (5)

Showing all 5 pathogenic / likely-pathogenic ClinVar records, ranked by ClinVar review status (expert panel → multiple submitters → single submitter), then by number of submitting labs.

Variant IDHGVSClassificationReviewSubmitters
3067139NM_021937.5(EEFSEC):c.1751_1752dup (p.Val585fs)Likely pathogeniccriteria provided, single submitter2
3067138NM_021937.5(EEFSEC):c.1169A>C (p.Asp390Ala)Likely pathogeniccriteria provided, single submitter1
4856243NM_021937.5(EEFSEC):c.1540G>T (p.Glu514Ter)Likely pathogeniccriteria provided, single submitter1
3764735NM_021937.5(EEFSEC):c.1A>G (p.Met1Val)Pathogenicno assertion criteria provided1
3764738NM_021937.5(EEFSEC):c.1278C>A (p.Cys426Ter)Pathogenicno assertion criteria provided1

Per-variant reference — Sugi Variant

Explore EEFSEC’s pathogenic and likely-pathogenic variants individually — each with its ClinVar classification and conditions, applied ACMG criteria (ClinGen expert panel, where curated), the calibrated in-silico predictors (AlphaMissense, REVEL, SaProt, conservation), gnomAD frequency, and the predictor-disagreement QC signal — on Sugi Variant.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 28 predictions of 1,546):

Position(s)EffectΔscoreSites
3:128246834–128246835acceptor_loss1.00005
3:128246835acceptor_gain1.0000
3:128246981donor_gain1.0000
3:128262225–128262226donor_loss1.00005
3:128341232acceptor_loss1.0000
3:128358201acceptor_gain1.0000
3:128358374–128358375donor_loss1.00003
3:128408067–128408068acceptor_loss1.00004
3:128153824–128153825donor_loss0.99006
3:128246830acceptor_gain0.9900

AlphaMissense

1,480 missense substitutions predicted likely pathogenic (of 3,898 scored), across 352 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
D9280.9980.999
H9680.9981.000
D1780.9940.997
D22980.9910.998
H1580.9900.998
D5080.9900.995
H23080.9880.998
D3780.9870.995
F5380.9831.000
F23280.9811.000
F52280.9780.999
F3680.9710.993
D11180.9680.996
H33680.9670.997
F49480.9630.993
D11880.9520.983
F50380.9500.995
F58180.9180.992
S4280.9120.994
D14980.9090.949

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

CancerPrognosticp-value
Lung Adenocarcinoma (TCGA)favorable0.000144
Rectum Adenocarcinoma (TCGA)favorable0.000221

Disease associations

OMIM: gene MIM:607695 | disease phenotypes: MIM:249500, MIM:613668, MIM:621102

GenCC curated gene-disease

2 curated gene-disease records:

DiseaseClassificationInheritanceRecords
neurodevelopmental disorderStrongAutosomal recessive
neurodevelopmental disorder with progressive spasticity and brain abnormalitiesLimitedAutosomal recessive

Genomics England panels (PanelApp)

Clinical diagnostic gene panels including this gene (9 panels, 9 green/diagnostic-grade). Confidence: green = diagnostic, amber = moderate.

9 panels:

PanelRating
Ataxia and cerebellar anomalies - childhood onsetgreen
Early onset or syndromic epilepsygreen
Fetal anomaliesgreen
Hereditary ataxia and cerebellar anomalies, childhood onsetgreen
Hypotonic infantgreen
Intellectual disabilitygreen
Leukodystrophy, childhood onsetgreen
Paediatric disordersgreen
Unexplained death in infancy and sudden unexplained death in childhoodgreen

Mondo (4): autosomal recessive non-syndromic intellectual disability (MONDO:0019502), infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly (MONDO:0013351), neurodevelopmental disorder with progressive spasticity and brain abnormalities (MONDO:0976233), neurodevelopmental disorder (MONDO:0700092)

Orphanet (2): Autosomal recessive non-syndromic intellectual disability (Orphanet:88616), Infantile cerebral and cerebellar atrophy with postnatal progressive microcephaly (Orphanet:402364)

HPO phenotypes

showing 60 of 80 phenotypes (HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000218High palate
HP:0000219Thin upper lip vermilion
HP:0000252Microcephaly
HP:0000276Long face
HP:0000347Micrognathia
HP:0000365Hearing impairment
HP:0000400Macrotia
HP:0000486Strabismus
HP:0000505Visual impairment
HP:0000568Microphthalmia
HP:0000609Optic nerve hypoplasia
HP:0000639Nystagmus
HP:0000641Dysmetric saccades
HP:0000657Oculomotor apraxia
HP:0000666Horizontal nystagmus
HP:0000750Delayed speech and language development
HP:0000767Pectus excavatum
HP:0001159Syndactyly
HP:0001250Seizure
HP:0001252Hypotonia
HP:0001257Spasticity
HP:0001260Dysarthria
HP:0001263Global developmental delay
HP:0001270Motor delay
HP:0001272Cerebellar atrophy
HP:0001317Abnormal cerebellum morphology
HP:0001321Cerebellar hypoplasia
HP:0001347Hyperreflexia
HP:0001382Joint hypermobility
HP:0001511Intrauterine growth retardation
HP:0001623Breech presentation
HP:0001643Patent ductus arteriosus
HP:0001684Secundum atrial septal defect
HP:0001762Talipes equinovarus
HP:0001945Fever
HP:0001999Abnormal facial shape
HP:0002015Dysphagia
HP:0002059Cerebral atrophy
HP:0002061Lower limb spasticity
HP:0002066Gait ataxia
HP:0002069Bilateral tonic-clonic seizure
HP:0002080Intention tremor
HP:0002104Apnea
HP:0002131Episodic ataxia
HP:0002133Status epilepticus
HP:0002164Nail dysplasia
HP:0002342Moderate intellectual disability
HP:0002376Developmental regression
HP:0002384Focal impaired awareness seizure
HP:0002445Tetraplegia
HP:0002804Arthrogryposis multiplex congenita
HP:0002808Kyphosis
HP:0003128Lactic acidosis
HP:0003259Elevated circulating creatinine concentration
HP:0003390Sensory axonal neuropathy
HP:0003577Congenital onset
HP:0004209Clinodactyly of the 5th finger
HP:0005484Secondary microcephaly
HP:0006829Severe muscular hypotonia

GWAS associations

showing 30 of 139 associations:

StudyTraitp-value
GCST007431_115Lung function (FEV1/FVC)7e-32
GCST002563_5Hypospadias1e-26
GCST90002404_476Red cell distribution width5e-18
GCST007692_23Chronic obstructive pulmonary disease4e-15
GCST004899_7Gestational age at birth (maternal effect)9e-15
GCST007800_97Asthma (childhood onset)4e-14
GCST004147_17Chronic obstructive pulmonary disease4e-13
GCST004898_1Preterm birth (maternal effect)2e-12
GCST90002393_369Monocyte count4e-12
GCST90002401_427Platelet distribution width1e-11
GCST004185_26Lung function (FEV1/FVC)6e-11
GCST002541_2Menarche (age at onset)1e-10
GCST007611_14Chronic obstructive pulmonary disease or high blood pressure (pleiotropy)9e-10
GCST010043_140Asthma5e-9
GCST010042_121Asthma6e-9
GCST007432_150FEV12e-8
GCST011320_12Type 2 diabetes or prostate cancer (pleiotropy)2e-8
GCST007656_9Chronic obstructive pulmonary disease or resting heart rate (pleiotropy)4e-8
GCST000880_4Menarche (age at onset)1e-7
GCST003262_1068Post bronchodilator FEV12e-7
GCST003262_310Post bronchodilator FEV12e-7
GCST003262_316Post bronchodilator FEV12e-7
GCST003262_1139Post bronchodilator FEV14e-7
GCST003262_1140Post bronchodilator FEV14e-7
GCST003262_1141Post bronchodilator FEV14e-7
GCST003262_325Post bronchodilator FEV14e-7
GCST003264_1121Post bronchodilator FEV1/FVC ratio4e-7
GCST003262_434Post bronchodilator FEV15e-7
GCST003264_1468Post bronchodilator FEV1/FVC ratio5e-7
GCST007797_45Asthma onset (childhood vs adult)5e-7

EFO canonical traits (from GWAS)

11 canonical traits:

EFO IDTrait name
EFO:0004703age at menarche
EFO:0004314forced expiratory volume
EFO:0004713FEV/FVC ratio
EFO:0003917premature birth
EFO:0005939parental genotype effect measurement
EFO:0005112gestational age
EFO:0004847age at onset
EFO:0003892pulmonary function measurement
EFO:0005091monocyte count
EFO:0007984platelet component distribution width
EFO:0009188Red cell distribution width

MeSH disease descriptors

1 disease descriptors:

DescriptorNameTree numbers
D065886Neurodevelopmental DisordersF03.625

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression3
Valproic Acidaffects expression, decreases methylation, increases expression3
sodium arsenitedecreases expression, increases expression2
Aflatoxin B1affects expression, decreases methylation2
aristolochic acid Idecreases expression1
potassium perchloratedecreases expression1
2-methyl-4-isothiazolin-3-onedecreases expression1
beta-lapachoneincreases expression1
butyraldehydedecreases expression1
tetrabromobisphenol Adecreases expression1
aflatoxin B2decreases methylation1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608affects binding, increases reaction1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
pentabrominated diphenyl ether 100decreases expression1
hexabrominated diphenyl ether 153decreases expression1
(+)-JQ1 compoundincreases expression1
Arsenic Trioxidedecreases response to substance1
Arsenicaffects methylation1
Cisplatindecreases expression1
Doxorubicindecreases expression1
Ivermectindecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Tretinoindecreases expression1
Urethanedecreases expression1
Cadmium Chloridedecreases expression1
Okadaic Aciddecreases expression1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

showing 60 of 210 trials:

NCTPhaseStatusTitle
NCT04586348Phase 4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115Phase 4UNKNOWNDouble-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT02559102Phase 3COMPLETEDDexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079Phase 3COMPLETEDStudy of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480Phase 3RECRUITINGReducing Missed Appointments
NCT07377032Phase 3RECRUITINGTAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02909959Phase 2COMPLETEDSulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348Phase 2RECRUITINGSertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372Phase 2COMPLETEDSafety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT00503191Phase 1COMPLETEDNeuroModulation Technique Treatment of Autism
NCT04475848Phase 1COMPLETEDA Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398Phase 1COMPLETEDIAMA-6 Oral Dose Study in Healthy Adults
NCT01783041Phase 2/3COMPLETEDEffect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385Phase 2/3COMPLETEDFetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098Early Phase 1NOT_YET_RECRUITINGCentral Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783Not specifiedCOMPLETEDCYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504Not specifiedRECRUITINGStudying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784Not specifiedUNKNOWNHigh Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791Not specifiedCOMPLETEDNutrition and Pregnancy Intervention Study
NCT01942525Not specifiedUNKNOWNInfluence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants
NCT02003170Not specifiedCOMPLETEDEtiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649Not specifiedCOMPLETEDEnhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191Not specifiedTERMINATEDBiomarkers, Neurodevelopment and Preterm Infants
NCT02690675Not specifiedCOMPLETEDIron Supplement Effect on Child Development
NCT02694003Not specifiedCOMPLETEDBetter Nights, Better Days for Children With Neurodevelopment Disorders
NCT02792894Not specifiedCOMPLETEDFamily Networks (FaNs) for Children With Developmental Disorders and Delays
NCT02871674Not specifiedUNKNOWNGood Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
NCT02887157Not specifiedCOMPLETEDAnalyzing Retinal Microanatomy in ROP
NCT02898298Not specifiedCOMPLETEDPositive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder
NCT02912780Not specifiedUNKNOWNIntroduction of Microsystems in a Level 3 Neonatal Intensive Care Unit
NCT03023293Not specifiedCOMPLETEDn-3 PUFAs, Irisin and Maternal Glucose Metabolism From Pregnancy to Postpartum
NCT03023644Not specifiedCOMPLETEDImproving Neurodevelopmental Outcomes in Children With Congenital Heart Disease: An Intervention Study
NCT03032991Not specifiedUNKNOWNEarly Biomarkers of Neurodevelopment in Offspring of Diabetic Mothers
NCT03088189Not specifiedTERMINATEDEffect of Parental Peri-conceptional Vitamin B12 Supplementation on Infant Neurocognitive Development in Offspring
NCT03096028Not specifiedCOMPLETEDDevelopmental Origins of Mental Health Disorders
NCT03148782Not specifiedCOMPLETEDBrain Plasticity Underlying Acquisition of New Organizational Skills in Children-R61 Phase
NCT03172104Not specifiedCOMPLETEDNeurobehavioural Development of Infants Born <30 Weeks Gestational Age Between Birth and Five Years of Age
NCT03222375Not specifiedRECRUITINGSQUED™ Series 28.1 Home-use and Treatment of Autowave Reverberator of Autism
NCT03229928Not specifiedCOMPLETEDClinical Testing of a Real-Time Behavior Measurement Tool: Measuring Outcomes for CHAnge
NCT03232489Not specifiedUNKNOWNStudy for the Evaluation of the Feasibility of Applying Advanced MRI Scanning in Pediatric Clinical Practice
NCT03381027Not specifiedCOMPLETEDBABY SMART (Study of Massage Therapy, Sleep And neurodevelopMenT)
NCT03388294Not specifiedCOMPLETEDEvaluation of a Novel Intervention for Infants At Risk for Neurodevelopmental Disorders
NCT03410810Not specifiedUNKNOWNChildhood Outcomes of Preterm Brain Abnormalities
NCT03492060Not specifiedRECRUITINGLongitudinal Study of Neurogenetic Disorders
NCT03577756Not specifiedCOMPLETEDNeurodevelopmental Assessment of Infants With Cystic Fibrosis
NCT03654248Not specifiedCOMPLETEDLet’s Get Organized in Adult Psychiatric/habilitation Care
NCT03659279Not specifiedCOMPLETEDLet’s Get Organized Feasibility Study
NCT03722615Not specifiedCOMPLETEDEpidemiology of Congenital Cytomegalovirus in a High HIV Prevalence Setting, South Africa
NCT03770832Not specifiedACTIVE_NOT_RECRUITINGWearable Sensors and Video Recordings to Monitor Motor Development
NCT03830879Not specifiedRECRUITINGShenzhen Birth Cohort Study
NCT03835689Not specifiedCOMPLETEDStrongest FamiliesTM Neurodevelopmental
NCT03882788Not specifiedCOMPLETEDThe Effect of Anesthesia on Neurodevelopmental Outcome (NDO)
NCT03922087Not specifiedCOMPLETEDNo-worry Baby Project
NCT03977259Not specifiedACTIVE_NOT_RECRUITINGTargeting Human Milk Fortification to Improve Preterm Infant Growth and Brain Development
NCT04043572Not specifiedUNKNOWNThe Biomarkers of Neurological Disease in Utero Study
NCT04096430Not specifiedRECRUITINGEvaluation of Effectiveness of Child-oriented Goal-setting in Paediatric Rehabilitation (the ENGAGE Approach)
NCT04108273Not specifiedCOMPLETEDBrain Plasticity Underlying Acquisition of New Organizational Skills in Children
NCT04201509Not specifiedCOMPLETEDValidity of Neurocognitive Assessment Methods in Childhood ADHD
NCT04233775Not specifiedUNKNOWNAltered Cerebral Growth and Development in Infants With Congenital Heart Disease
NCT04313283Not specifiedCOMPLETEDTranslating Peer-to-Peer Support Into a Clinical Setting