Is EBF3 p.Val82Met (c.244G>A) pathogenic?

EBF3 p.Val82Met (c.244G>A) is classified Uncertain significance in EBF3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-26). AlphaMissense: likely pathogenic (0.9776); No allele count reported in gnomAD v4.1 (AN 1,593,310); Associated with EBF3-related disorder.

What condition is associated with EBF3 p.Val82Met (c.244G>A)?

EBF3 p.Val82Met (c.244G>A) is associated with EBF3-related disorder (ClinVar).

How common is EBF3 p.Val82Met (c.244G>A) in the general population?

EBF3 p.Val82Met (c.244G>A) is no allele count reported in gnomAD v4.1 (AN 1,593,310) (gnomAD).

What do computational predictors say about EBF3 p.Val82Met (c.244G>A)?

AlphaMissense predicts likely pathogenic (score 0.9776) — an in-silico prediction, not a clinical call.

EBF3 p.Val82Met

c.244G>A · rs2493680911 · VCV2631651

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9776 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,593,310)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Conditions

EBF3-related disorder

Computational evidence

Protein change
AlphaMissense	0.9776	likely pathogenic
REVEL	0.334	indeterminate
SaProt	LLR -10.68	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.2	GERP 2.3, phastCons 1
Regional constraint	o/e 0.59	unconstrained · MANE · 4,677 bp · p 1e-06 · regional, not allelic
Overall
CADD	27.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,593,310). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: EBF3
Protein: p.Val82Met
Coding: c.244G>A
MANE Select: NM_001375380
dbSNP: rs2493680911
Type: single nucleotide variant
Location: chr10:129963414 (GRCh38)
Gene constraint: LOEUF 0.353 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 71.89 · 2 PDB

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

Disease context

EBF3-related disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EBF3 p.Arg404Ter Pathogenic/Likely pathogenic ★★ same condition
EBF3 c.1194+1G>C Likely pathogenic ★ same condition
EBF3 p.Arg163Pro Likely pathogenic ★ same condition
EBF3 p.Cys161Arg Likely pathogenic ★ same condition
EBF3 p.Met232Lys Likely pathogenic ★ same condition
EBF3 p.Val82fs Pathogenic ★ same residue
EBF3 c.1373-10A>G Likely benign same condition
EBF3 c.412-7C>T Likely benign 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-val82met (accessed [today's date]).

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