Is CTSD p.Ala337= (c.1011G>A) pathogenic?

CTSD p.Ala337= (c.1011G>A) is classified Likely benign in CTSD (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-20). Ultra-rare (popmax 0.0165%, sas); Associated with neuronal ceroid lipofuscinosis.

What condition is associated with CTSD p.Ala337= (c.1011G>A)?

CTSD p.Ala337= (c.1011G>A) is associated with neuronal ceroid lipofuscinosis (ClinVar).

How common is CTSD p.Ala337= (c.1011G>A) in the general population?

CTSD p.Ala337= (c.1011G>A) is ultra-rare (popmax 0.0165%, sas) (gnomAD).

CTSD p.Ala337=

c.1011G>A · rs761661648 · VCV2140070

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, sas)

Conditions

neuronal ceroid lipofuscinosis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.042	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -2.7
Overall
CADD	2.756	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0165% South Asian · 15/91,054 alleles

Filtering AF 0.0101% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00811%

Overall 0.00353% 57/1,613,510 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0165%	6,070
Middle Eastern	0.0164%	6,084
Remaining individualsnot grpmax-eligible	0.0032%	31,226
European (non-Finnish)	0.00314%	31,885
African / African-American	0.00267%	37,446

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.Ala337=
Coding: c.1011G>A
MANE Select: NM_001909
dbSNP: rs761661648
Type: single nucleotide variant
Location: chr11:1753863 (GRCh38)
Gene constraint: LOEUF 0.886 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.69 · 9 PDB
Residue 337: a disulfide bond; the peptidase a1 domain; an α-helix

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.Ala337Ser Uncertain significance ★ ⚠ same residue
CTSD p.Ala337Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
CTSD p.Ala337Val 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

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-ala337 (accessed [today's date]).

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