Is AGK p.Ser382fs (c.1141_1142dup) pathogenic?

AGK p.Ser382fs (c.11411142dup) is classified Pathogenic/Likely pathogenic in AGK (ClinVar, Multiple submitters, 2 submitters; last evaluated 2022-10-28). Absent from gnomAD; Associated with cataract 38.

What condition is associated with AGK p.Ser382fs (c.1141_1142dup)?

AGK p.Ser382fs (c.1141_1142dup) is associated with cataract 38, Sengers syndrome (ClinVar).

How common is AGK p.Ser382fs (c.1141_1142dup) in the general population?

AGK p.Ser382fs (c.1141_1142dup) is absent from gnomAD (gnomAD).

How is Early onset non-syndromic cataract inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

AGK p.Ser382fs

c.1141_1142dup · rs1554405928 · VCV524160

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

cataract 38

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function; NMD-escape possible for C-terminal truncations
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -11	GERP -10
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: AGK
Protein: p.Ser382fs
Coding: c.1141_1142dup
MANE Select: NM_018238
dbSNP: rs1554405928
Type: Duplication
Location: chr7:141652792 (GRCh38)
Gene constraint: LOEUF 0.918 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 86.93 · 2 PDB
Residue 382: a UniProt-annotated variant site (in mtdps10)

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

Disease context

cataract 38 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Sengers syndrome

For Early onset non-syndromic cataract (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Infancy, Neonatal

Similar variants

AGK c.424-3dup Benign/Likely benign ★★ same condition
AGK c.1046_1046+1dup Pathogenic ★ same condition
AGK p.Ile120fs Pathogenic ★ same condition
AGK p.Ile346fs Pathogenic ★ same condition
AGK p.Ile348fs Pathogenic ★ same condition
AGK p.Tyr390fs Pathogenic ★ same condition
AGK c.101+4_101+7dup Likely benign ★ same condition
AGK c.975+16dup Benign ★ 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/agk-p-ser382fs (accessed [today's date]).

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