Is EBP p.Arg63del (c.183GCG[1]) pathogenic?

EBP p.Arg63del (c.183GCG[1]) is classified Conflicting classifications of pathogenicity in EBP (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2023-12-10). Absent from gnomAD; Associated with EBP-related disorders.

What condition is associated with EBP p.Arg63del (c.183GCG[1])?

EBP p.Arg63del (c.183GCG[1]) is associated with EBP-related disorders (ClinVar).

How common is EBP p.Arg63del (c.183GCG[1]) in the general population?

EBP p.Arg63del (c.183GCG[1]) is absent from gnomAD (gnomAD).

EBP p.Arg63del

c.183GCG[1] · rs2519522250 · VCV2737221

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

EBP-related disorders

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.9	GERP 0.95, phastCons 1

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: EBP
Protein: p.Arg63del
Coding: c.183GCG[1]
MANE Select: NM_001378122 · reported on NM_006579
dbSNP: rs2519522250
Type: Microsatellite
Location: chrX:48523953 (GRCh38)
Structure: AlphaFold pLDDT 59.09
Residue 63: 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.Arg63Ter Pathogenic ★ same residue
EBP p.Arg63Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
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.Thr168fs 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/ebp-p-arg63del (accessed [today's date]).

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