EEFSEC

eukaryotic elongation factor, selenocysteine-tRNA specific

Basic information

Region (hg38): 3:128153481-128408646

Links

ENSG00000132394 ∙ NCBI:60678 ∙ OMIM:607695 ∙ HGNC:24614 ∙ Uniprot:P57772 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense		1	89	6	3	99
nonsense	1					1
start loss	1					1
frameshift		1				1
splice donor/acceptor (+/-2bp)						0
Total	2	2	89	8	4

Highest pathogenic variant AF is 0.00000656711

GnomAD

Source: gnomAD

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: 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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Eefsec

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