Is SYNRG p.Val1193= (c.3579G>C) pathogenic?

SYNRG p.Val1193= (c.3579G>C) is classified Likely benign in SYNRG (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-28). No allele count reported in gnomAD v4.1 (AN 1,614,020); Associated with SYNRG-related disorder.

What condition is associated with SYNRG p.Val1193= (c.3579G>C)?

SYNRG p.Val1193= (c.3579G>C) is associated with SYNRG-related disorder (ClinVar).

How common is SYNRG p.Val1193= (c.3579G>C) in the general population?

SYNRG p.Val1193= (c.3579G>C) is no allele count reported in gnomAD v4.1 (AN 1,614,020) (gnomAD).

SYNRG p.Val1193=

c.3579G>C · rs2547878731 · VCV3053579

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,614,020)

Conditions

SYNRG-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.63	GERP -0.71, phastCons 1
Overall
CADD	8.563	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,614,020). 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: SYNRG
Protein: p.Val1193=
Coding: c.3579G>C
MANE Select: NM_007247
dbSNP: rs2547878731
Type: single nucleotide variant
Location: chr17:37536066 (GRCh38)
Gene constraint: LOEUF 0.38 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 48.74 · 1 PDB

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

Disease context

SYNRG-related disorder

Similar variants

SYNRG c.372-1G>A Uncertain significance ★ same condition
SYNRG p.Phe1094Val Uncertain significance ★ ⚠ same condition
SYNRG p.Asp572Glu Uncertain significance ⚠ same condition
SYNRG p.Glu1080Lys Uncertain significance same condition
SYNRG p.Gly49Arg Uncertain significance ⚠ same condition
SYNRG c.3518-6C>T Likely benign same condition
SYNRG p.Asp182Asn Likely benign ⚠ same condition
SYNRG p.Ile1213= Likely benign 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/synrg-p-val1193 (accessed [today's date]).

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