Is CTSD c.*19G>A pathogenic?

CTSD c.19G>A is classified Benign/Likely benign in CTSD (ClinVar, Multiple submitters, 4 submitters; last evaluated 2024-11-14). Low-frequency (popmax 1.56%, afr); Associated with neuronal ceroid lipofuscinosis 10.

What condition is associated with CTSD c.*19G>A?

CTSD c.*19G>A is associated with neuronal ceroid lipofuscinosis 10 (ClinVar).

How common is CTSD c.*19G>A in the general population?

CTSD c.*19G>A is low-frequency (popmax 1.56%, afr) (gnomAD).

How is CLN10 disease inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

CTSD c.*19G>A

rs201434721 · VCV137046

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.56%, afr)

Conditions

neuronal ceroid lipofuscinosis 10

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 -13
Overall
CADD	0.138	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.56% African / African-American · 1,169/75,014 alleles

Filtering AF 1.48% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.45%

Overall 0.0908% 1,464/1,612,858 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.56%	64
Admixed American	0.0833%	1,200
Remaining individualsnot grpmax-eligible	0.08%	1,250
Middle Eastern	0.0165%	6,060
European (non-Finnish)	0.0164%	6,113
South Asian	0.0011%	91,080

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
Coding: c.*19G>A
MANE Select: NM_001909
dbSNP: rs201434721
Type: single nucleotide variant
Location: chr11:1753484 (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 10 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For CLN10 disease (Orphanet):

Inheritance: Autosomal recessive
Onset: Adult, Antenatal, Infancy

Similar variants

CTSD c.*210C>G Uncertain significance ★★ same condition
CTSD p.Ala239Val Uncertain significance ★★ ⚠ same condition
CTSD p.Arg411His Uncertain significance ★★ ⚠ same condition
CTSD p.Glu310Lys Uncertain significance ★★ ⚠ same condition
CTSD p.Gly316Arg Uncertain significance ★★ ⚠ same condition
CTSD p.Gly362Arg Uncertain significance ★★ ⚠ same condition
CTSD p.His273Tyr Uncertain significance ★★ ⚠ same condition
CTSD p.Ile198Val 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-c-star-19g-a (accessed [today's date]).

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