Is EBF3 p.Arg51Ter (c.151_153delinsTGA) pathogenic?

EBF3 p.Arg51Ter (c.151153delinsTGA) is classified Pathogenic in EBF3 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-12-07). No gnomAD frequency available for this variant.

How common is EBF3 p.Arg51Ter (c.151_153delinsTGA) in the general population?

EBF3 p.Arg51Ter (c.151_153delinsTGA) is no gnomAD frequency available for this variant (gnomAD).

EBF3 p.Arg51Ter

c.151_153delinsTGA · rs1554937249 · VCV503921

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 2 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 3.7	GERP 2.3, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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.Arg51Ter
Coding: c.151_153delinsTGA
MANE Select: NM_001375380
dbSNP: rs1554937249
Type: Indel
Location: chr10:129963505 (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

Similar variants

EBF3 p.Arg51Trp Uncertain significance ★ ⚠ same residue
EBF3 p.Arg51= Likely benign ★ same residue
EBF3 c.782-4_782-3delinsAG Uncertain significance ★ same type
EBF3 p.Met208_Phe211delinsIle Uncertain significance ★ same type

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-arg51ter (accessed [today's date]).

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