EEFSEC

eukaryotic elongation factor, selenocysteine-tRNA specific

Basic information

Region (hg38): 3:128153480-128408646

Links

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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1	1	2
missense		1	44		3	48
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	2	44	1	4

Variants in EEFSEC

This is a list of pathogenic ClinVar variants found in the EEFSEC region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-128153517-C-T		not specified	Uncertain significance (Apr 01, 2024)
3-128153562-G-A		not specified	Uncertain significance (Apr 13, 2022)
3-128153621-G-T		not specified	Uncertain significance (Feb 15, 2024)
3-128153637-G-C		not specified	Uncertain significance (Feb 27, 2024)
3-128153640-C-G		not specified	Uncertain significance (Jan 26, 2023)
3-128153651-G-T			Likely benign (May 01, 2022)
3-128153683-C-A		not specified	Uncertain significance (May 31, 2023)
3-128153688-C-T		not specified	Uncertain significance (May 28, 2024)
3-128153694-C-T		not specified	Uncertain significance (Nov 18, 2023)
3-128153751-G-A		not specified	Uncertain significance (Jan 23, 2023)
3-128153818-T-A		not specified	Uncertain significance (May 23, 2024)
3-128246949-G-T		not specified	Uncertain significance (Nov 03, 2023)
3-128246961-A-G		not specified	Uncertain significance (Dec 27, 2023)
3-128246973-C-T		not specified	Uncertain significance (Sep 12, 2023)
3-128247007-T-G		not specified	Uncertain significance (Dec 07, 2023)
3-128247024-A-G		not specified	Uncertain significance (Dec 27, 2022)
3-128262133-G-A		not specified	Uncertain significance (Aug 18, 2023)
3-128262142-C-T		not specified	Uncertain significance (Jan 22, 2024)
3-128262143-G-A			Benign (Apr 19, 2018)
3-128262153-G-T		not specified	Uncertain significance (Feb 15, 2023)
3-128262219-A-G		not specified	Uncertain significance (Jun 22, 2023)
3-128262220-T-C		not specified	Uncertain significance (Nov 13, 2023)
3-128264687-G-A		not specified	Uncertain significance (Sep 22, 2023)
3-128264734-T-A		not specified	Uncertain significance (Jan 23, 2023)
3-128341257-C-A		not specified	Uncertain significance (Sep 07, 2022)

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