Is EBF3 p.Pro180fs (c.537_544del) pathogenic?

EBF3 p.Pro180fs (c.537544del) is classified Pathogenic in EBF3 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-01-18). No gnomAD frequency available for this variant; Associated with Inborn genetic diseases.

What condition is associated with EBF3 p.Pro180fs (c.537_544del)?

EBF3 p.Pro180fs (c.537_544del) is associated with Inborn genetic diseases (ClinVar).

How common is EBF3 p.Pro180fs (c.537_544del) in the general population?

EBF3 p.Pro180fs (c.537_544del) is no gnomAD frequency available for this variant (gnomAD).

EBF3 p.Pro180fs

c.537_544del · rs2493627848 · VCV2265788

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 6 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.4, 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.Pro180fs
Coding: c.537_544del
MANE Select: NM_001375380
dbSNP: rs2493627848
Type: Deletion
Location: chr10:129957268 (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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EBF3 p.Pro180His Uncertain significance ★ ⚠ same residue
EBF3 p.Thr477fs Pathogenic ★★ same condition
EBF3 c.289_291+1del Pathogenic ★ same condition
EBF3 p.Gln113fs Pathogenic ★ same condition
EBF3 c.1373-2del Uncertain significance ★ same condition
EBF3 p.Lys168del Uncertain significance ★ same condition
EBF3 p.Pro180Ser Uncertain significance ★ ⚠ same residue
EBF3 p.Tyr391_Met393delinsLeu Uncertain significance ★ 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-pro180fs (accessed [today's date]).

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