GeneBe

EBF3

EBF transcription factor 3, the group of MicroRNA protein coding host genes|IPT domain containing|Early B-cell factors

Basic information

Region (hg38): 10:129835233-129973053

Links

ENSG00000108001 ∙ NCBI:253738 ∙ OMIM:607407 ∙ HGNC:19087 ∙ Uniprot:Q9H4W6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

  • hypotonia, ataxia, and delayed development syndrome (Strong), mode of inheritance: AD
  • hypotonia, ataxia, and delayed development syndrome (Definitive), mode of inheritance: AD
  • hypotonia, ataxia, and delayed development syndrome (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Hypotonia, ataxia, and delayed development syndrome (HADDS)ADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Genitourinary; Neurologic28017370; 28017372; 28017373

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EBF3 gene.

  • not_provided (140 variants)
  • Hypotonia,_ataxia,_and_delayed_development_syndrome (95 variants)
  • Inborn_genetic_diseases (62 variants)
  • EBF3-related_disorder (23 variants)
  • Intellectual_disability (8 variants)
  • not_specified (8 variants)
  • See_cases (4 variants)
  • Autism_spectrum_disorder (3 variants)
  • Global_developmental_delay (3 variants)
  • Expressive_language_delay (2 variants)
  • Hypotonia (2 variants)
  • Ataxia (2 variants)
  • Neurodevelopmental_disorder (2 variants)
  • Generalized_hypotonia (2 variants)
  • Growth_abnormality (1 variants)
  • Broad-based_gait (1 variants)
  • Recurrent_urinary_tract_infections (1 variants)
  • Developmental_regression (1 variants)
  • Oromandibular-limb_hypogenesis_spectrum (1 variants)
  • Constipation (1 variants)
  • Isolated_Pierre-Robin_syndrome (1 variants)
  • Intellectual_disability,_X-linked_102 (1 variants)
  • Renal_tubular_dysgenesis (1 variants)
  • EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)
  • Abnormal_facial_shape (1 variants)
  • Neurogenic_bladder (1 variants)
  • Vesicoureteral_reflux (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EBF3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001375380.1. 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
5
clinvar
32
clinvar
2
clinvar
 39
missense
13
clinvar
33
clinvar
106
clinvar
10
clinvar
 162
nonsense
13
clinvar
4
clinvar
 17
start loss
0
frameshift
17
clinvar
9
clinvar
6
clinvar
 32
splice donor/acceptor (+/-2bp)
8
clinvar
3
clinvar
3
clinvar
 14
Total 51 49 120 42 2

Highest pathogenic variant AF is 0.00000786819

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
EBF3protein_codingprotein_codingENST00000368648 16128559
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
1.000.0000667125543011255440.00000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.611633540.4600.00002103612
Missense in Polyphen3896.7140.39291950
Synonymous0.5001461540.9490.00001111061
Loss of Function5.05131.70.03160.00000166342

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000008810.00000881
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Transcriptional activator (PubMed:28017373, PubMed:28017372, PubMed:28017370). Recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). {ECO:0000250|UniProtKB:Q07802, ECO:0000269|PubMed:28017370, ECO:0000269|PubMed:28017372, ECO:0000269|PubMed:28017373}.;
Pathway
Differentiation of white and brown adipocyte (Consensus)

Recessive Scores

pRec
0.108

Intolerance Scores

loftool
0.0389
rvis_EVS
-0.65
rvis_percentile_EVS
16.44

Haploinsufficiency Scores

pHI
0.136
hipred
Y
hipred_score
0.773
ghis
0.558

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.996

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Ebf3
Phenotype
nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Gene ontology

Biological process
multicellular organism development;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
Cellular component
nucleus
Molecular function
RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;metal ion binding;protein dimerization activity