Is CHST3 p.Glu384fs (c.1150_1166del) pathogenic?

CHST3 p.Glu384fs (c.11501166del) is classified Pathogenic in CHST3 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-14). Absent from gnomAD; Associated with spondyloepiphyseal dysplasia with congenital joint dislocations.

What condition is associated with CHST3 p.Glu384fs (c.1150_1166del)?

CHST3 p.Glu384fs (c.1150_1166del) is associated with spondyloepiphyseal dysplasia with congenital joint dislocations (ClinVar).

How common is CHST3 p.Glu384fs (c.1150_1166del) in the general population?

CHST3 p.Glu384fs (c.1150_1166del) is absent from gnomAD (gnomAD).

How is CHST3-related skeletal dysplasia inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

CHST3 p.Glu384fs

c.1150_1166del · rs2131776376 · VCV1452559

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

spondyloepiphyseal dysplasia with congenital joint dislocations

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	escapes	premature termination codon in the last exon (3 of 3) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -1.3	GERP -3.8

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: CHST3
Protein: p.Glu384fs
Coding: c.1150_1166del
MANE Select: NM_004273
dbSNP: rs2131776376
Type: Deletion
Location: chr10:72008178 (GRCh38)
Gene constraint: LOEUF 1.119 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.58

Full CHST3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

spondyloepiphyseal dysplasia with congenital joint dislocations — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For CHST3-related skeletal dysplasia (Orphanet):

Inheritance: Autosomal recessive
Onset: Antenatal, Neonatal

Similar variants

CHST3 p.Glu384Gly Uncertain significance ★ ⚠ same residue
CHST3 p.Ala261fs Likely pathogenic ★ same condition
CHST3 p.Asp66fs Likely pathogenic ★ same condition
CHST3 p.Leu255fs Pathogenic ★ same condition
CHST3 p.Leu286fs Pathogenic ★ same condition
CHST3 p.Pro392_Leu393insTer Pathogenic ★ same condition
CHST3 p.Ser79_Leu80insTer Pathogenic ★ same condition
CHST3 p.Gly316fs 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/chst3-p-glu384fs (accessed [today's date]).

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