Is SYNJ1 p.Pro1090= (c.3270A>G) pathogenic?

SYNJ1 p.Pro1090= (c.3270A>G) is classified Likely benign in SYNJ1 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-04-01). Ultra-rare (popmax 0.0179%, mid); Associated with developmental and epileptic encephalopathy, 53.

How common is SYNJ1 p.Pro1090= (c.3270A>G) in the general population?

SYNJ1 p.Pro1090= (c.3270A>G) is ultra-rare (popmax 0.0179%, mid) (gnomAD).

SYNJ1 p.Pro1090=

Q: What condition is associated with SYNJ1 p.Pro1090= (c.3270A>G)?

SYNJ1 p.Pro1090= (c.3270A>G) is associated with developmental and epileptic encephalopathy, 53, early-onset Parkinson disease 20 (ClinVar).

c.3270A>G · rs1299635688 · VCV1091449

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0179%, mid)

Conditions

developmental and epileptic encephalopathy, 53

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -4.3	GERP -2.8
Overall
CADD	3.017	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0179% Middle Eastern · 1/5,588 alleles

Filtering AF 0.000195% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000128%

Overall 0.000545% 8/1,467,972 alleles · ultra-rare exomes 6/1,315,792 · genomes 2/152,180 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0179%	5,588
Remaining individualsnot grpmax-eligible	0.00177%	56,342
European (non-Finnish)	0.000542%	184,605

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: SYNJ1
Protein: p.Pro1090=
Coding: c.3270A>G
MANE Select: NM_203446
dbSNP: rs1299635688
Type: single nucleotide variant
Location: chr21:32645767 (GRCh38)
Gene constraint: LOEUF 0.539 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.09 · 5 PDB
Residue 1090: the 'disordered' region

Full SYNJ1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

developmental and epileptic encephalopathy, 53 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: early-onset Parkinson disease 20

Similar variants

SYNJ1 p.Pro1090Ser Uncertain significance ★ same residue
SYNJ1 c.1201-2A>G Likely pathogenic ★★ same condition
SYNJ1 c.2461+2T>C Likely pathogenic ★★ same condition
SYNJ1 c.3478+1G>A Likely pathogenic ★★ same condition
SYNJ1 p.Arg219Gln Pathogenic ★★ same condition
SYNJ1 p.Arg534Ter Pathogenic/Likely pathogenic ★★ same condition
SYNJ1 p.Arg709Ter Pathogenic/Likely pathogenic ★★ same condition
SYNJ1 p.Gln748Ter 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/synj1-p-pro1090 (accessed [today's date]).

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