Is CTSF p.Leu5= (c.15G>T) pathogenic?

CTSF p.Leu5= (c.15G>T) is classified Likely benign in CTSF (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-07). Very rare (popmax 0.000982%, nfe); Associated with neuronal ceroid lipofuscinosis 13.

What condition is associated with CTSF p.Leu5= (c.15G>T)?

CTSF p.Leu5= (c.15G>T) is associated with neuronal ceroid lipofuscinosis 13 (ClinVar).

How common is CTSF p.Leu5= (c.15G>T) in the general population?

CTSF p.Leu5= (c.15G>T) is very rare (popmax 0.000982%, nfe) (gnomAD).

CTSF p.Leu5=

c.15G>T · VCV3687925

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000982%, nfe)

Conditions

neuronal ceroid lipofuscinosis 13

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 2.1	GERP -0.075, phastCons 1
Overall
CADD	13.59	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000982% European (non-Finnish) · 11/1,119,754 alleles

Filtering AF 0.000527% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000385%

Overall 0.000833% 11/1,320,252 alleles · very rare

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: CTSF
Protein: p.Leu5=
Coding: c.15G>T
MANE Select: NM_003793
Type: single nucleotide variant
Location: chr11:66568472 (GRCh38)
Gene constraint: LOEUF 1.296 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 82.78 · 1 PDB

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

Disease context

neuronal ceroid lipofuscinosis 13 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For CLN13 disease (Orphanet):

Onset: Adolescent, Adult, Childhood, Elderly

Similar variants

CTSF p.Leu5Pro Uncertain significance ★ ⚠ same residue
CTSF c.1045+1G>T Likely pathogenic ★★ same condition
CTSF p.Ala22Ser Uncertain significance ★★ ⚠ same condition
CTSF p.Arg196Gln Uncertain significance ★★ ⚠ same condition
CTSF p.Arg205Trp Uncertain significance ★★ ⚠ same condition
CTSF p.Arg413Cys Uncertain significance ★★ ⚠ same condition
CTSF p.Gly415Arg Uncertain significance ★★ ⚠ same condition
CTSF p.Gly439Ser 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/ctsf-p-leu5 (accessed [today's date]).

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