Is CHAT p.Ala392= (c.1176G>A) pathogenic?

CHAT p.Ala392= (c.1176G>A) is classified Likely benign in CHAT (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-18). Very rare (popmax 0.00267%, afr); Associated with congenital myasthenic syndrome 6.

What condition is associated with CHAT p.Ala392= (c.1176G>A)?

CHAT p.Ala392= (c.1176G>A) is associated with congenital myasthenic syndrome 6 (ClinVar).

How common is CHAT p.Ala392= (c.1176G>A) in the general population?

CHAT p.Ala392= (c.1176G>A) is very rare (popmax 0.00267%, afr) (gnomAD).

CHAT p.Ala392=

c.1176G>A · rs200321426 · VCV2806580

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

Conditions

congenital myasthenic syndrome 6

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 -4.5	GERP -4.1
Overall
CADD	5.263	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00267% African / African-American · 2/74,930 alleles

Filtering AF 0.00153% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0013%

Overall 0.00173% 28/1,614,100 alleles · very rare exomes 27/1,461,870 · genomes 1/152,230 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00267%	37,465
European (non-Finnish)	0.0022%	45,386

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: CHAT
Protein: p.Ala392=
Coding: c.1176G>A
MANE Select: NM_020549
dbSNP: rs200321426
Type: single nucleotide variant
Location: chr10:49646569 (GRCh38)
Gene constraint: LOEUF 0.973 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 84.73 · 8 PDB
Residue 392: a UniProt-annotated variant site (sequence variant); an α-helix

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

Disease context

congenital myasthenic syndrome 6 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CHAT p.Ala392Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
CHAT p.Ala392Val Uncertain significance ★ ⚠ same residue
CHAT c.1282-2A>T Likely pathogenic ★★ same condition
CHAT c.1840-9A>G Pathogenic/Likely pathogenic ★★ same condition
CHAT c.698+1G>T Likely pathogenic ★★ same condition
CHAT c.698+2T>C Likely pathogenic ★★ same condition
CHAT p.Ala557Thr Pathogenic/Likely pathogenic ★★ same condition
CHAT p.Arg151Ter 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/chat-p-ala392 (accessed [today's date]).

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