Is SYN2 p.Pro107Ser (c.319C>T) pathogenic?

SYN2 p.Pro107Ser (c.319C>T) is classified Uncertain significance in SYN2 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-07-22). AlphaMissense: likely benign (0.07); No allele count reported in gnomAD v4.1 (AN 571,368); Associated with schizophrenia.

What condition is associated with SYN2 p.Pro107Ser (c.319C>T)?

SYN2 p.Pro107Ser (c.319C>T) is associated with schizophrenia (ClinVar).

How common is SYN2 p.Pro107Ser (c.319C>T) in the general population?

SYN2 p.Pro107Ser (c.319C>T) is no allele count reported in gnomAD v4.1 (AN 571,368) (gnomAD).

What do computational predictors say about SYN2 p.Pro107Ser (c.319C>T)?

AlphaMissense predicts likely benign (score 0.07) — an in-silico prediction, not a clinical call.

SYN2 p.Pro107Ser

c.319C>T · VCV3892587

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.07 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 571,368)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

schizophrenia

Computational evidence

Protein change
AlphaMissense	0.07	likely benign
REVEL	0.016	strongly benign-leaning
SaProt	LLR -8.10	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.88	GERP -3.5, phastCons 0.95
Regional constraint	o/e 1.02	unconstrained · MANE · 186 kb · p 0.66 · regional, not allelic
Overall
CADD	14.78	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 571,368). 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: SYN2
Protein: p.Pro107Ser
Coding: c.319C>T
MANE Select: NM_133625
Type: single nucleotide variant
Location: chr3:12004870 (GRCh38)
Gene constraint: LOEUF 0.539 · pLI 0.90 (gnomAD)
Structure: AlphaFold pLDDT 75.24
Residue 107: the 'b; linker' region

Full SYN2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

schizophrenia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TIMP4 p.Glu107Ala Uncertain significance ★ ⚠ same residue
SYN2 p.Gln529Ter Uncertain significance ★ same condition
SYN2 p.Ala54Val Benign ★★ same type
SYN2 p.Thr506Ala Benign ★★ same type
SYN2 c.1369+21G>C Uncertain significance ★ same type
SYN2 p.Ala302Gly Uncertain significance ★ same type
SYN2 p.Ala546Gly Uncertain significance ★ ⚠ same type
SYN2 p.Arg179Gln Uncertain significance ★ ⚠ same type

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/syn2-p-pro107ser (accessed [today's date]).

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