Is CTSD p.Ile47Met (c.141T>G) pathogenic?

CTSD p.Ile47Met (c.141T>G) is classified Uncertain significance in CTSD (ClinVar, Single submitter, 1 submitter; last evaluated 2018-10-20). AlphaMissense: likely benign (0.0887); Absent from gnomAD v4.1; Associated with neuronal ceroid lipofuscinosis.

What condition is associated with CTSD p.Ile47Met (c.141T>G)?

CTSD p.Ile47Met (c.141T>G) is associated with neuronal ceroid lipofuscinosis (ClinVar).

How common is CTSD p.Ile47Met (c.141T>G) in the general population?

CTSD p.Ile47Met (c.141T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CTSD p.Ile47Met (c.141T>G)?

AlphaMissense predicts likely benign (score 0.0887) — an in-silico prediction, not a clinical call.

CTSD p.Ile47Met

c.141T>G · rs545927559 · VCV641902

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0887 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

neuronal ceroid lipofuscinosis

Computational evidence

Protein change
AlphaMissense	0.0887	likely benign
REVEL	0.089	moderately benign-leaning
SaProt	LLR -6.48	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -2.1	GERP -2
Regional constraint	o/e 0.87	unconstrained · MANE · 10 kb · p 0.0029 · regional, not allelic
Overall
CADD	1.179	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CTSD
Protein: p.Ile47Met
Coding: c.141T>G
dbSNP: rs545927559
Type: single nucleotide variant
Location: chr11:1761396 (GRCh38)

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

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-ile47met (accessed [today's date]).

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