EEFSEC
Basic information
Region (hg38): 3:128153481-128408646
Links
Phenotypes
GenCC
Source:
- neurodevelopmental disorder with progressive spasticity and brain abnormalities (Limited), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 3 | |||||
missense | 89 | 99 | ||||
nonsense | 1 | |||||
start loss | 1 | 1 | ||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 2 | 2 | 89 | 8 | 4 |
Highest pathogenic variant AF is 0.00000656711
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
EEFSEC | protein_coding | protein_coding | ENST00000254730 | 7 | 255189 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.70e-8 | 0.499 | 125701 | 0 | 47 | 125748 | 0.000187 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.635 | 325 | 359 | 0.906 | 0.0000211 | 3861 |
Missense in Polyphen | 84 | 114.28 | 0.73502 | 1250 | ||
Synonymous | 0.312 | 152 | 157 | 0.968 | 0.00000998 | 1244 |
Loss of Function | 0.977 | 14 | 18.5 | 0.755 | 8.76e-7 | 225 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000119 | 0.000119 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000661 | 0.000653 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000265 | 0.000264 |
Middle Eastern | 0.000661 | 0.000653 |
South Asian | 0.0000328 | 0.0000327 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
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