Is STRADA p.Phe53del (c.158_160del) pathogenic?

STRADA p.Phe53del (c.158160del) is classified Uncertain significance in STRADA (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-02). Absent from gnomAD; Associated with polyhydramnios, megalencephaly, and symptomatic epilepsy.

What condition is associated with STRADA p.Phe53del (c.158_160del)?

STRADA p.Phe53del (c.158_160del) is associated with polyhydramnios, megalencephaly, and symptomatic epilepsy (ClinVar).

How common is STRADA p.Phe53del (c.158_160del) in the general population?

STRADA p.Phe53del (c.158_160del) is absent from gnomAD (gnomAD).

STRADA p.Phe53del

Q: How is Polyhydramnios-megalencephaly-symptomatic epilepsy syndrome inherited?

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

c.158_160del · rs2143920802 · VCV1474678

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

polyhydramnios, megalencephaly, and symptomatic epilepsy

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 12	GERP 1.8, 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: STRADA
Protein: p.Phe53del
Coding: c.158_160del
MANE Select: NM_001003787
dbSNP: rs2143920802
Type: Deletion
Location: chr17:63714072 (GRCh38)
Gene constraint: LOEUF 0.649 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.46 · 4 PDB

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

Disease context

polyhydramnios, megalencephaly, and symptomatic epilepsy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Polyhydramnios-megalencephaly-symptomatic epilepsy syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Antenatal, Infancy, Neonatal

Similar variants

STRADA p.Phe53fs Pathogenic ★ same residue
STRADA p.Lys18fs Pathogenic ★ same condition
STRADA p.Pro34fs Pathogenic ★ same condition
STRADA p.Val277fs Pathogenic ★ same condition
STRADA p.His342fs Uncertain significance ★ same condition
STRADA p.Ile382fs Uncertain significance ★ same condition
STRADA p.Pro364fs Uncertain significance ★ same condition
STRADA p.Val318_Ser324del 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/strada-p-phe53del (accessed [today's date]).

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