EEFSEC

protein-coding

eukaryotic elongation factor, selenocysteine-tRNA specific

Gene summary

Enables GTPase activity. Involved in selenocysteine incorporation. Predicted to be located in cytoplasm and nucleus. Predicted to be part of ribonucleoprotein complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_021937.5

Inheritance

ClinVar variants

P:6U:109B:12

Top phenotype

neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr3:128,153,481-128,408,646

External References & Databases

Ensembl (ENSG00000132394)

Transcript & Mutation Effects

hg38 • Region Span ~255.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

neurodevelopmental disorder with progressive spasticity and brain abnormalitiesLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0976233

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to EEFSEC variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 105

not providedTotal: 9

Neurodevelopmental disorder with progressive spasticity and brain abnormalitiesTotal: 7

Infantile cerebral and cerebellar atrophy with postnatal progressive microcephalyTotal: 1

Autosomal recessive non-syndromic intellectual disabilityTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021937.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	2 clinvar	1 clinvar	5
missense		2 clinvar	104 clinvar	6 clinvar	3 clinvar	115
nonsense	1 clinvar	1 clinvar	1 clinvar			3
start loss	1 clinvar					1
frameshift		1 clinvar				1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	2	4	109	8	4	127

Highest pathogenic variant AF is 0.0000075246194

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021937.5	RefSeq	NP_068756.2	7	MANE Select
ENST00000254730.11	Ensembl	ENSP00000254730.5	7	MANE Select
NM_001437809.1	RefSeq	NP_001424738.1	8	Standard
NM_001437810.1	RefSeq	NP_001424739.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Selenium Metabolism and Selenoproteins
Selenocysteine synthesis
Metabolism of amino acids and derivatives
Metabolism
Selenoamino acid metabolism

Biological Process

selenocysteine incorporation
translational elongation

Molecular Function

tRNA binding
translation elongation factor activity
GTPase activity
GTP binding
selenocysteine insertion sequence binding

Cellular Component

nucleus
cytoplasm
ribonucleoprotein complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000254730
Coding exons: 7
Length: 255189
Individuals with no LoFs: 125701
Homozygous LoFs: 0
Heterozygous LoFs: 47
Defined: 125748
p: 0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.635	325	359	0.906	0.0000211	3861
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00066	0.00065	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00026	0.00026	rare
South Asian	0.000033	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.270

Intolerance Scores

LoFtool: 0.613
RVIS EVS: -0.38
RVIS percentile EVS: 28.11

Essentials

Essential (CRISPR): E
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.710

Gene Damage Prediction

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