Is CTSD p.Val156= (c.468G>A) pathogenic?

CTSD p.Val156= (c.468G>A) is classified Likely benign in CTSD (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-12). Very rare (popmax 8.52e-05%, nfe); Associated with neuronal ceroid lipofuscinosis.

What condition is associated with CTSD p.Val156= (c.468G>A)?

CTSD p.Val156= (c.468G>A) is associated with neuronal ceroid lipofuscinosis (ClinVar).

How common is CTSD p.Val156= (c.468G>A) in the general population?

CTSD p.Val156= (c.468G>A) is very rare (popmax 8.52e-05%, nfe) (gnomAD).

CTSD p.Val156=

c.468G>A · rs2493825776 · VCV2712789

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.52e-05%, nfe)

Conditions

neuronal ceroid lipofuscinosis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.036	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.19	GERP 0.24, phastCons 0.97
Overall
CADD	7.783	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.52e-05% European (non-Finnish) · 1/1,173,488 alleles

Overall 6.87e-05% 1/1,454,578 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: CTSD
Protein: p.Val156=
Coding: c.468G>A
MANE Select: NM_001909
dbSNP: rs2493825776
Type: single nucleotide variant
Location: chr11:1758972 (GRCh38)
Gene constraint: LOEUF 0.886 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.69 · 9 PDB
Residue 156: a disulfide bond; a β-strand; the peptidase a1 domain

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

Similar variants

CTSD p.Val156fs Pathogenic ★ same residue
CTSD p.Val156Met Uncertain significance ★ same residue
CTSD c.228+1G>A Likely pathogenic ★★ same condition
CTSD p.Glu82Ter Pathogenic/Likely pathogenic ★★ same condition
CTSD c.828-3C>A Uncertain significance ★★ same condition
CTSD p.Ala10Ser Uncertain significance ★★ ⚠ same condition
CTSD p.Ala18Pro Uncertain significance ★★ ⚠ same condition
CTSD p.Ala18Thr 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-val156 (accessed [today's date]).

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