Is CHAT p.Pro301= (c.903T>C) pathogenic?

CHAT p.Pro301= (c.903T>C) is classified Benign in CHAT (ClinVar, Multiple submitters, 5 submitters; last evaluated 2026-02-03). Common (popmax 5%, afr) — too common for a highly-penetrant pathogenic allele; Associated with congenital myasthenic syndrome 6.

What condition is associated with CHAT p.Pro301= (c.903T>C)?

CHAT p.Pro301= (c.903T>C) is associated with congenital myasthenic syndrome 6 (ClinVar).

CHAT p.Pro301=

Q: How common is CHAT p.Pro301= (c.903T>C) in the general population?

CHAT p.Pro301= (c.903T>C) is common (popmax 5%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.903T>C · rs113897064 · VCV128727

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

gnomAD v4.1

Common

common (popmax 5%, afr) — too common for a highly-penetrant pathogenic allele

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 -12	GERP -4.7
Overall
CADD	0.04	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 5% African / African-American · 3,732/74,596 alleles

Filtering AF 4.87% ClinGen BA1/BS1 input FAF95, joint · FAF99 4.81%

Overall 0.268% 4,260/1,589,482 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	5%	20
Remaining individualsnot grpmax-eligible	0.372%	269
Admixed American	0.368%	272
Middle Eastern	0.199%	503
South Asian	0.016%	6,264
European (non-Finnish)	0.00565%	17,684

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.Pro301=
Coding: c.903T>C
MANE Select: NM_020549
dbSNP: rs113897064
Type: single nucleotide variant
Location: chr10:49625623 (GRCh38)
Gene constraint: LOEUF 0.973 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 84.73 · 8 PDB

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-pro301 (accessed [today's date]).

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