Is CHAT p.Asn192= (c.576C>T) pathogenic?

CHAT p.Asn192= (c.576C>T) is classified Benign in CHAT (ClinVar, Single submitter, 2 submitters; last evaluated 2026-01-31). Rare (popmax 0.586%, afr); Associated with congenital myasthenic syndrome 6.

What condition is associated with CHAT p.Asn192= (c.576C>T)?

CHAT p.Asn192= (c.576C>T) is associated with congenital myasthenic syndrome 6 (ClinVar).

How common is CHAT p.Asn192= (c.576C>T) in the general population?

CHAT p.Asn192= (c.576C>T) is rare (popmax 0.586%, afr) (gnomAD).

CHAT p.Asn192=

c.576C>T · rs150236872 · VCV461460

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.586%, 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	<0.2	all four deltas below 0.2 · C>G here scores Δ0.64 · evaluated, not missing
Constraint at this position
Conservation	phyloP 0.8	GERP -4.3, phastCons 1
Overall
CADD	9.788	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.586% African / African-American · 439/74,924 alleles

Filtering AF 0.541% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.523%

Overall 0.0307% 495/1,610,814 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.586%	171
Remaining individualsnot grpmax-eligible	0.0465%	2,152
Admixed American	0.0336%	2,974
Middle Eastern	0.033%	3,030
European (non-Finnish)	0.000424%	235,800

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.Asn192=
Coding: c.576C>T
MANE Select: NM_020549
dbSNP: rs150236872
Type: single nucleotide variant
Location: chr10:49619913 (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 192: a β-strand

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 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
CHAT p.Arg207Gly Likely pathogenic ★★ same condition
CHAT p.Arg207His 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-asn192 (accessed [today's date]).

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