Is CTSD p.Leu11fs (c.17_30dup) pathogenic?

CTSD p.Leu11fs (c.1730dup) is classified Pathogenic in CTSD (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-03-06). Absent from gnomAD; Associated with neuronal ceroid lipofuscinosis.

What condition is associated with CTSD p.Leu11fs (c.17_30dup)?

CTSD p.Leu11fs (c.17_30dup) is associated with neuronal ceroid lipofuscinosis, neuronal ceroid lipofuscinosis 10 (ClinVar).

How common is CTSD p.Leu11fs (c.17_30dup) in the general population?

CTSD p.Leu11fs (c.17_30dup) is absent from gnomAD (gnomAD).

CTSD p.Leu11fs

c.17_30dup · rs2133668728 · VCV1322174

Pathogenic Multiple submitters

Classification

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

neuronal ceroid lipofuscinosis

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 1 of 9
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.84	GERP -1.7, phastCons 0.36

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: CTSD
Protein: p.Leu11fs
Coding: c.17_30dup
MANE Select: NM_001909
dbSNP: rs2133668728
Type: Duplication
Location: chr11:1763829 (GRCh38)
Gene constraint: LOEUF 0.886 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.69 · 9 PDB

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

Disease context

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

Also linked: neuronal ceroid lipofuscinosis 10

Similar variants

CTSD c.675_704+1dup Likely pathogenic ★ same condition
CTSD p.Ala314fs Pathogenic ★ same condition
CTSD p.Glu352fs Pathogenic ★ same condition
CTSD p.Lys253fs Pathogenic ★ same condition
CTSD p.Val156fs Pathogenic ★ same condition
CTSD p.Val174fs Pathogenic ★ same condition
CTSD c.972+4_972+5dup Uncertain significance ★ same condition
CTSD p.Glu278_Val279insGlu 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/ctsd-p-leu11fs (accessed [today's date]).

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