NAGA

Chr 22AR

alpha-N-acetylgalactosaminidase

Also known as: D22S674, GALB

NCBI Gene: 4668ENSG00000198951UniProt: P17050OMIM: 104170

The protein removes terminal alpha-N-acetylgalactosamine residues from glycolipids and glycopeptides in lysosomes, functioning as a critical enzyme for glycolipid breakdown. Mutations cause Schindler disease (types I, II, and III) and Kanzaki disease, with type I presenting as severe infantile neuroaxonal dystrophy and type II (Kanzaki disease) manifesting as a milder adult-onset angiokeratoma disorder. These conditions follow autosomal recessive inheritance.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 1.303 OMIM phenotypes
Clinical Summary— NAGA
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Gene-Disease Validity (ClinGen)
alpha-N-acetylgalactosaminidase deficiency · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

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Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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ClinVar Variants
61 unique Pathogenic / Likely Pathogenic· 131 VUS of 381 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.30LOEUF
pLI 0.000
Z-score 0.51
OE 0.88 (0.61–1.30)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.17Z-score
OE missense 0.97 (0.87–1.08)
237 obs / 244.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.88 (0.61–1.30)
0≤0.351.4
Missense OE0.97 (0.87–1.08)
0≤0.61.4
Synonymous OE0.88
0≤1.21.6
LoF obs/exp: 18 / 20.5Missense obs/exp: 237 / 244.5Syn Z: 0.90

ClinVar Variant Classifications

381 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic45
Likely Pathogenic16
VUS131
Likely Benign136
Benign32
Conflicting14
45
Pathogenic
16
Likely Pathogenic
131
VUS
136
Likely Benign
32
Benign
14
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
16
0
29
0
45
Likely Pathogenic
12
2
2
0
16
VUS
3
96
31
1
131
Likely Benign
0
1
66
69
136
Benign
0
1
30
1
32
Conflicting
—14
Total3110015871374

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

NAGA · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients