Is EBP p.Ser98fs (c.292_296del) pathogenic?

EBP p.Ser98fs (c.292296del) is classified Pathogenic in EBP (ClinVar, Single submitter, 1 submitter; last evaluated 2013-02-08). Absent from gnomAD; Associated with X-linked chondrodysplasia punctata 2.

What condition is associated with EBP p.Ser98fs (c.292_296del)?

EBP p.Ser98fs (c.292_296del) is associated with X-linked chondrodysplasia punctata 2 (ClinVar).

How common is EBP p.Ser98fs (c.292_296del) in the general population?

EBP p.Ser98fs (c.292_296del) is absent from gnomAD (gnomAD).

How is X-linked dominant chondrodysplasia punctata inherited?

Typically X-linked dominant (Orphanet). A genetic counselor can assess individual risk for a family.

EBP p.Ser98fs

c.292_296del · rs587783604 · VCV158536

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

X-linked chondrodysplasia punctata 2

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 7.8	GERP 2, 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: EBP
Protein: p.Ser98fs
Coding: c.292_296del
MANE Select: NM_001378122 · reported on NM_006579
dbSNP: rs587783604
Type: Deletion
Location: chrX:48524062 (GRCh38)
Structure: AlphaFold pLDDT 59.09
Residue 98: the 'disordered' region

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

Disease context

X-linked chondrodysplasia punctata 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For X-linked dominant chondrodysplasia punctata (Orphanet):

Inheritance: X-linked dominant
Onset: Antenatal, Infancy, Neonatal
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

EBP p.Ser98Phe Pathogenic/Likely pathogenic ★★ ⚠ same residue
EBP p.Ala54fs Likely pathogenic ★ same condition
EBP p.Ser98Pro Uncertain significance ★ ⚠ same residue
EBP p.Pro131fs Pathogenic same condition
EBP p.Arg110Gln Pathogenic/Likely pathogenic ★★ same condition
EBP p.Arg110Ter Pathogenic ★★ same condition
EBP p.Arg147His Pathogenic ★★ ⚠ same condition
EBP p.Arg62Trp Pathogenic/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-ser98fs (accessed [today's date]).

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