Is EBF3 p.Arg209Trp (c.625C>T) pathogenic?

EBF3 p.Arg209Trp (c.625C>T) is classified Pathogenic/Likely pathogenic in EBF3 (ClinVar, Multiple submitters, 9 submitters; last evaluated 2024-03-01). AlphaMissense: likely pathogenic (0.9998); Absent from gnomAD v4.1; Associated with hypotonia, ataxia, and delayed development syndrome.

What condition is associated with EBF3 p.Arg209Trp (c.625C>T)?

EBF3 p.Arg209Trp (c.625C>T) is associated with hypotonia, ataxia, and delayed development syndrome (ClinVar).

How common is EBF3 p.Arg209Trp (c.625C>T) in the general population?

EBF3 p.Arg209Trp (c.625C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about EBF3 p.Arg209Trp (c.625C>T)?

AlphaMissense predicts likely pathogenic (score 0.9998) — an in-silico prediction, not a clinical call.

EBF3 p.Arg209Trp

c.625C>T · rs779003155 · VCV375494

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

AlphaMissense

likely pathogenic

0.9998 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

hypotonia, ataxia, and delayed development syndrome

Computational evidence

Protein change
AlphaMissense	0.9998	likely pathogenic ✓ concordant with ClinVar
REVEL	0.724	pathogenic-leaning
SaProt	LLR -15.79	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 12	GERP 0.69, phastCons 1
Regional constraint	o/e 0.16	constrained · MANE · 85 kb · p 4.3e-15 · regional, not allelic
Overall
CADD	34.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: EBF3
Protein: p.Arg209Trp
Coding: c.625C>T
MANE Select: NM_001375380
dbSNP: rs779003155
Type: single nucleotide variant
Location: chr10:129877779 (GRCh38)
Gene constraint: LOEUF 0.353 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 71.89 · 2 PDB
Residue 209: a UniProt-annotated variant site (in hadds; significant loss of transcriptional activator activity; localizes both in the cytoplasm and the nucleus; decreased chromatin-binding)

Full EBF3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hypotonia, ataxia, and delayed development syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EBF3 p.Arg209Gln Pathogenic/Likely pathogenic ★★ same residue
EBF3 c.486-1G>A Pathogenic ★★ same condition
EBF3 c.555-2A>G Likely pathogenic ★★ same condition
EBF3 p.Arg163Gln Pathogenic ★★ same condition
EBF3 p.Arg163Leu Pathogenic ★★ same condition
EBF3 p.Arg163Trp Pathogenic/Likely pathogenic ★★ same condition
EBF3 p.Arg206Ter Pathogenic ★★ same condition
EBF3 p.Arg312Ter Pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/ebf3-p-arg209trp (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown