Is SYN1 p.Pro437fs (c.1310del) pathogenic?

SYN1 p.Pro437fs (c.1310del) is classified Pathogenic in SYN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-12-09). No gnomAD frequency available for this variant; Associated with Inborn genetic diseases.

What condition is associated with SYN1 p.Pro437fs (c.1310del)?

SYN1 p.Pro437fs (c.1310del) is associated with Inborn genetic diseases (ClinVar).

How common is SYN1 p.Pro437fs (c.1310del) in the general population?

SYN1 p.Pro437fs (c.1310del) is no gnomAD frequency available for this variant (gnomAD).

SYN1 p.Pro437fs

c.1310del · rs1569322834 · VCV588529

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

Inborn genetic diseases

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 11 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -9.4

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.Pro437fs
Coding: c.1310del
MANE Select: NM_006950
dbSNP: rs1569322834
Type: Deletion
Location: chrX:47574771 (GRCh38)
Structure: AlphaFold pLDDT 69.86
Residue 437: the 'disordered' region; the 'd; pro-rich linker' region

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SYN1 p.His38_Ala42del Uncertain significance ★★ same condition
SYN1 p.Pro437Gln Uncertain significance ★ ⚠ same residue
SYN1 p.Pro437Leu Uncertain significance ★ ⚠ same residue
SYN1 p.Pro437= Likely benign ★ same residue
SYN1 p.Ala441Asp Uncertain significance ★★ ⚠ same condition
SYN1 p.Arg169Trp Uncertain significance ★★ ⚠ same condition
SYN1 p.Arg424Trp Uncertain significance ★★ ⚠ same condition
SYN1 p.Gly320Ala 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/syn1-p-pro437fs (accessed [today's date]).

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