Is SYN1 p.Arg420fs (c.1258dup) pathogenic?

SYN1 p.Arg420fs (c.1258dup) is classified Pathogenic in SYN1 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-12-29). No gnomAD frequency available for this variant; Associated with epilepsy, X-linked 1, with variable learning disabilities and behavior disorders.

What condition is associated with SYN1 p.Arg420fs (c.1258dup)?

SYN1 p.Arg420fs (c.1258dup) is associated with epilepsy, X-linked 1, with variable learning disabilities and behavior disorders (ClinVar).

How common is SYN1 p.Arg420fs (c.1258dup) in the general population?

SYN1 p.Arg420fs (c.1258dup) is no gnomAD frequency available for this variant (gnomAD).

SYN1 p.Arg420fs

Q: How is X-linked epilepsy-learning disabilities-behavior disorders syndrome inherited?

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

c.1258dup · rs2519685866 · VCV1700042

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

epilepsy, X-linked 1, with variable learning disabilities and behavior disorders

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	predicted	premature termination codon in exon 10 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 5.8	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: SYN1
Protein: p.Arg420fs
Coding: c.1258dup
MANE Select: NM_006950
dbSNP: rs2519685866
Type: Duplication
Location: chrX:47575174 (GRCh38)
Structure: AlphaFold pLDDT 69.86
Residue 420: the 'c; actin-binding and synaptic-vesicle binding' region; the 'disordered' region

Full SYN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

epilepsy, X-linked 1, with variable learning disabilities and behavior disorders — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For X-linked epilepsy-learning disabilities-behavior disorders syndrome (Orphanet):

Inheritance: X-linked recessive
Onset: Childhood

Similar variants

SYN1 p.Arg420Gln Likely pathogenic ★★ ⚠ same residue
SYN1 p.Arg420Gly Uncertain significance ★★ ⚠ same residue
SYN1 p.Arg420Trp Conflicting classifications of pathogenicity ★ ⚠ same residue
SYN1 p.Leu481fs Pathogenic/Likely pathogenic ★★ same condition
SYN1 p.Leu205_Gln206insLeu Uncertain significance ★★ same condition
SYN1 p.Ala441fs Pathogenic ★ same condition
SYN1 p.Gln421fs Pathogenic ★ same condition
SYN1 p.Gln562fs 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/syn1-p-arg420fs (accessed [today's date]).

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