Is AGRN p.Ser1022= (c.3066A>G) pathogenic?

AGRN p.Ser1022= (c.3066A>G) is classified Benign in AGRN (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-02-04). Common (popmax 96.7%, eas) — too common for a highly-penetrant pathogenic allele; Associated with congenital myasthenic syndrome 8.

What condition is associated with AGRN p.Ser1022= (c.3066A>G)?

AGRN p.Ser1022= (c.3066A>G) is associated with congenital myasthenic syndrome 8 (ClinVar).

AGRN p.Ser1022=

Q: How common is AGRN p.Ser1022= (c.3066A>G) in the general population?

AGRN p.Ser1022= (c.3066A>G) is common (popmax 96.7%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.3066A>G · rs2465128 · VCV128297

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

gnomAD v4.1

Common

common (popmax 96.7%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

congenital myasthenic syndrome 8

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 -1.6	GERP -2.6
Overall
CADD	0.122	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 96.7% East Asian · 43,336/44,830 alleles

Filtering AF 95.9% ClinGen BA1/BS1 input FAF95, joint · FAF99 95.6%

Overall 89.2% 1,437,262/1,610,386 alleles · common

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	98.6%	1
East Asiangrpmax	96.7%	1
Finnishnot grpmax-eligible	93%	1
European (non-Finnish)	91.3%	1
Admixed American	91.3%	1
South Asian	88.7%	1
Ashkenazi Jewishnot grpmax-eligible	88.6%	1
Remaining individualsnot grpmax-eligible	87.9%	1
Middle Eastern	82.3%	1
African / African-American	50.2%	2

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: AGRN
Protein: p.Ser1022=
Coding: c.3066A>G
MANE Select: NM_198576
dbSNP: rs2465128
Type: single nucleotide variant
Location: chr1:1046551 (GRCh38)
Gene constraint: LOEUF 0.73 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 69.79 · 1 PDB
Residue 1022: the 'disordered' region

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

Disease context

congenital myasthenic syndrome 8 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

AGRN p.Ser1022Thr Uncertain significance ★ same residue
AGRN p.Ser1022Leu Uncertain significance ★ same residue
AGRN c.3632-1G>C Likely pathogenic ★★ same condition
AGRN p.Arg1671Ter Pathogenic/Likely pathogenic ★★ same condition
AGRN p.Arg834Ter Pathogenic/Likely pathogenic ★★ same condition
AGRN p.Gly1582Arg Pathogenic ★★ same condition
AGRN p.Gly1675Ser Pathogenic/Likely pathogenic ★★ same condition
AGRN c.1177+4A>G Uncertain significance ★★ 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/agrn-p-ser1022 (accessed [today's date]).

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