Is GRN p.Ser262fs (c.784_787del) pathogenic?

GRN p.Ser262fs (c.784787del) is classified Pathogenic in GRN (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-29). No gnomAD frequency available for this variant; Associated with neuronal ceroid lipofuscinosis 11.

What condition is associated with GRN p.Ser262fs (c.784_787del)?

GRN p.Ser262fs (c.784_787del) is associated with neuronal ceroid lipofuscinosis 11, GRN-related frontotemporal lobar degeneration with Tdp43 inclusions (ClinVar).

How common is GRN p.Ser262fs (c.784_787del) in the general population?

GRN p.Ser262fs (c.784_787del) is no gnomAD frequency available for this variant (gnomAD).

GRN p.Ser262fs

c.784_787del · rs2510056456 · VCV2119142

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

neuronal ceroid lipofuscinosis 11

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 8 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.29	GERP -0.85, phastCons 0.06

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: GRN
Protein: p.Ser262fs
Coding: c.784_787del
MANE Select: NM_002087
dbSNP: rs2510056456
Type: Deletion
Location: chr17:44351112 (GRCh38)
Gene constraint: LOEUF 0.59 · pLI 0.04 (gnomAD)
Structure: AlphaFold pLDDT 76.74 · 8 PDB

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

Disease context

neuronal ceroid lipofuscinosis 11 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: GRN-related frontotemporal lobar degeneration with Tdp43 inclusions

For CLN11 disease (Orphanet):

Onset: Adolescent, Infancy

Similar variants

GRN p.Ser262Pro Uncertain significance ★★ ⚠ same residue
GRN p.Arg198fs Pathogenic ★★ same condition
GRN p.Asp128fs Pathogenic/Likely pathogenic ★★ same condition
GRN p.Cys157fs Pathogenic ★★ same condition
GRN p.Gln130fs Pathogenic ★★ same condition
GRN p.Gln337fs Pathogenic/Likely pathogenic ★★ same condition
GRN p.Gly35fs Pathogenic ★★ same condition
GRN p.Ser226fs 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/grn-p-ser262fs (accessed [today's date]).

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