EBF3 p.Thr276=
c.828G>A · rs2493991710 · VCV2441161
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Conditions
1
hypotonia, ataxia, and delayed development syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.38 | GERP -2.1, phastCons 0.076 |
| Overall | ||
| CADD | 11.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Filtering AF
7.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000434%
7/1,614,250 alleles · ultra-rare
exomes 7/1,461,872 · genomes 0/152,378 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
| South Asian | 0.0011% | 91,084 |
| European (non-Finnish) | 0.000339% | 295,012 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- EBF3
- Protein
- p.Thr276=
- Coding
- c.828G>A
- MANE Select
- NM_001375380
- dbSNP
- rs2493991710
- Type
- single nucleotide variant
- Location
- chr10:129867866 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 71.89 · 2 PDB
- Residue 276
- the ipt/tig domain
Similar variants
- EBF3 p.Thr276Met Uncertain significance ★ 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.Arg209Gln Pathogenic/Likely 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-thr276 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown