Is SYN1 p.Cys370= (c.1110C>T) pathogenic?

SYN1 p.Cys370= (c.1110C>T) is classified Benign/Likely benign in SYN1 (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-01-28). Rare (popmax 0.344%, afr); Associated with Inborn genetic diseases.

What condition is associated with SYN1 p.Cys370= (c.1110C>T)?

SYN1 p.Cys370= (c.1110C>T) is associated with Inborn genetic diseases, epilepsy, X-linked 1, with variable learning disabilities and behavior disorders (ClinVar).

How common is SYN1 p.Cys370= (c.1110C>T) in the general population?

SYN1 p.Cys370= (c.1110C>T) is rare (popmax 0.344%, afr) (gnomAD).

SYN1 p.Cys370=

c.1110C>T · rs141925310 · VCV207463

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.344%, afr)

Conditions

Inborn genetic diseases

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 -3.8
Overall
CADD	0.033	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.344% African / African-American · 196/56,999 alleles

Filtering AF 0.304% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.289%

Overall 0.0185% 222/1,202,995 alleles · rare exomes 116/1,091,076 · genomes 106/111,919 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.344%	291
Middle Eastern	0.023%	4,346
Admixed American	0.0178%	5,634
Remaining individualsnot grpmax-eligible	0.0148%	6,762
European (non-Finnish)	0.00112%	89,160

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: SYN1
Protein: p.Cys370=
Coding: c.1110C>T
MANE Select: NM_006950
dbSNP: rs141925310
Type: single nucleotide variant
Location: chrX:47576179 (GRCh38)
Structure: AlphaFold pLDDT 69.86
Residue 370: the 'c; actin-binding and synaptic-vesicle binding' 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

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

Similar variants

SYN1 p.Cys370Trp Uncertain significance ★★ ⚠ same residue
SYN1 p.Cys370Ter Likely pathogenic ★ same residue
SYN1 c.528-2A>T Pathogenic/Likely pathogenic ★★ same condition
SYN1 c.838-2A>G Likely pathogenic ★★ same condition
SYN1 p.Arg234Ter Pathogenic ★★ same condition
SYN1 p.Arg420Gln Likely pathogenic ★★ ⚠ same condition
SYN1 p.Arg422Ter Pathogenic ★★ same condition
SYN1 p.Gln483Ter 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-cys370 (accessed [today's date]).

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