Is EBP p.Thr168fs (c.501del) pathogenic?

EBP p.Thr168fs (c.501del) is classified Likely pathogenic in EBP (ClinVar, Single submitter, 1 submitter; last evaluated 2020-08-11). Associated with EBP-related disorders.

What condition is associated with EBP p.Thr168fs (c.501del)?

EBP p.Thr168fs (c.501del) is associated with EBP-related disorders (ClinVar).

EBP p.Thr168fs

c.501del · VCV4950388

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

EBP-related disorders

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-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4	GERP 2.1, phastCons 1

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

Variant & gene context

Gene: EBP
Protein: p.Thr168fs
Coding: c.501del
MANE Select: NM_001378122 · reported on NM_006579
Type: Deletion
Location: chrX:48528265 (GRCh38)
Structure: AlphaFold pLDDT 59.09
Residue 168: the 'disordered' region

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

Disease context

EBP-related disorders

Similar variants

EBP c.301+2_301+3del Likely pathogenic ★★ same condition
EBP p.Arg147His Pathogenic ★★ ⚠ same condition
EBP p.Gly161Arg Likely pathogenic ★★ same condition
EBP c.338+1G>A Pathogenic ★ same condition
EBP p.Gly161Glu Likely pathogenic ★ same condition
EBP p.Arg63del Conflicting classifications of pathogenicity ★ same condition
SH3D19 c.1534+9A>G Benign same condition
SH3D19 c.2083-245G>A 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/ebp-p-thr168fs (accessed [today's date]).

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