EEFSEC

eukaryotic elongation factor, selenocysteine-tRNA specific

Basic information

Region (hg38): 3:128153481-128408646

Links

ENSG00000132394NCBI:60678OMIM:607695HGNC:24614Uniprot:P57772AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • neurodevelopmental disorder with progressive spasticity and brain abnormalities (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EEFSEC gene.

  • not_specified (96 variants)
  • not_provided (5 variants)
  • Neurodevelopmental_disorder_with_progressive_spasticity_and_brain_abnormalities (5 variants)
  • Infantile_cerebral_and_cerebellar_atrophy_with_postnatal_progressive_microcephaly (1 variants)
  • Autosomal_recessive_non-syndromic_intellectual_disability (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EEFSEC gene is commonly pathogenic or not. These statistics are base on transcript: NM_000021937.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
1
clinvar
3
missense
1
clinvar
89
clinvar
6
clinvar
3
clinvar
99
nonsense
1
clinvar
1
start loss
1
1
frameshift
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
Total 2 2 89 8 4

Highest pathogenic variant AF is 0.00000656711

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EEFSECprotein_codingprotein_codingENST00000254730 7255189
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
2.70e-80.4991257010471257480.000187
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6353253590.9060.00002113861
Missense in Polyphen84114.280.735021250
Synonymous0.3121521570.9680.000009981244
Loss of Function0.9771418.50.7558.76e-7225

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001190.000119
Ashkenazi Jewish0.000.00
East Asian0.0006610.000653
Finnish0.000.00
European (Non-Finnish)0.0002650.000264
Middle Eastern0.0006610.000653
South Asian0.00003280.0000327
Other0.0001630.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Translation factor necessary for the incorporation of selenocysteine into proteins. It probably replaces EF-Tu for the insertion of selenocysteine directed by the UGA codon. SelB binds GTP and GDP.;
Pathway
Selenium Metabolism and Selenoproteins;Selenocysteine synthesis;Metabolism of amino acids and derivatives;Metabolism;Selenoamino acid metabolism (Consensus)

Recessive Scores

pRec
0.270

Intolerance Scores

loftool
0.613
rvis_EVS
-0.38
rvis_percentile_EVS
28.11

Haploinsufficiency Scores

pHI
0.266
hipred
N
hipred_score
0.394
ghis
0.514

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
S
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.710

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Eefsec
Phenotype

Gene ontology

Biological process
selenocysteine incorporation;translational elongation
Cellular component
nucleus;cytoplasm;ribonucleoprotein complex
Molecular function
tRNA binding;translation elongation factor activity;GTPase activity;GTP binding;selenocysteine insertion sequence binding;ribonucleoprotein complex binding