Is CSDE1 p.Ile158fs (c.472_476del) pathogenic?

CSDE1 p.Ile158fs (c.472476del) is classified Likely pathogenic in CSDE1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-19). Associated with CSDE1-related neurodevelopmental disorder.

What condition is associated with CSDE1 p.Ile158fs (c.472_476del)?

CSDE1 p.Ile158fs (c.472_476del) is associated with CSDE1-related neurodevelopmental disorder (ClinVar).

CSDE1 p.Ile158fs

c.472_476del · VCV4293955

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

CSDE1-related neurodevelopmental disorder

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 LoF-intolerant gene
NMD	predicted	premature termination codon in exon 6 of 20
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.9	GERP -0.26, phastCons 1

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

Variant & gene context

Gene: CSDE1
Protein: p.Ile158fs
Coding: c.472_476del
MANE Select: NM_001007553
Type: Microsatellite
Location: chr1:114736782 (GRCh38)
Gene constraint: LOEUF 0.295 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 80.05 · 5 PDB
Residue 158: the csd 2; truncated domain

Full CSDE1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CSDE1-related neurodevelopmental disorder

Similar variants

CSDE1 p.Gln712Ter Likely pathogenic ★ same condition
CSDE1 p.Phe719fs Likely pathogenic ★ same condition
CSDE1 p.Arg324Ter Uncertain significance ★ same condition
CSDE1 p.Arg774His Uncertain significance ★ ⚠ same condition
CSDE1 p.Met1Val Uncertain significance ★ same condition
CSDE1 p.Pro779Arg Uncertain significance ★ ⚠ same condition
CSDE1 p.Tyr16fs Uncertain significance ★ same condition
CSDE1 p.Arg77Ter 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/csde1-p-ile158fs (accessed [today's date]).

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