EBF3

Chr 10AD

EBF transcription factor 3

Also known as: COE3, EBF-3, HADDS, O/E-2, OE-2

NCBI Gene: 253738ENSG00000108001UniProt: Q9H4W6OMIM: 607407

This gene encodes a member of the early B-cell factor (EBF) family of DNA binding transcription factors. EBF proteins are involved in B-cell differentiation, bone development and neurogenesis, and may also function as tumor suppressors. The encoded protein inhibits cell survival through the regulation of genes involved in cell cycle arrest and apoptosis, and aberrant methylation or deletion of this gene may play a role in multiple malignancies including glioblastoma multiforme and gastric carcinoma. [provided by RefSeq, Sep 2011]

GeneReviewsOMIMResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Hypotonia, ataxia, and delayed development syndromeMIM #617330
AD

Clinical highlights

Gene-disease validity (ClinGen)
hypotonia, ataxia, and delayed development syndrome · ADDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
1
Active trials
24
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.15
LOEUF· LoF intol.
LOF
Mechanism· G2P
📖
GeneReview available — EBF3
Authoritative clinical overview · Recommended first read
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Dual constrained — LoF & missense intolerant
LoF Constraint?
0.15LOEUF
pLI 1.000
Z-score 5.05
OE 0.03 (0.01–0.15)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint?
3.61Z-score
OE missense 0.46 (0.40–0.52)
163 obs / 354.3 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios?
LoF OE?0.03 (0.01–0.15)
0≤0.351.4
Missense OE?0.46 (0.40–0.52)
0≤0.61.4
Synonymous OE?0.95
0≤1.21.6
LoF obs/exp: 1 / 31.7Missense obs/exp: 163 / 354.3Syn Z: 0.50

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

EBF3 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients