NAGPA

N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase

Basic information

Region (hg38): 16:5024844-5034141

Links

ENSG00000103174

∙ NCBI:51172 ∙ OMIM:607985 ∙ HGNC:17378 ∙ Uniprot:Q9UK23 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NAGPA gene.

not_specified (95 variants)
not_provided (11 variants)
NAGPA-related_disorder (11 variants)
Stuttering,_familial_persistent,_2 (2 variants)
Variant_of_unknown_significance (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAGPA gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016256.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				11 clinvar	2 clinvar	13
missense			93 clinvar	8 clinvar	2 clinvar	103
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	94	19	4

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAGPA	protein_coding	protein_coding	ENST00000312251	10	9298

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.01e-12	0.0797	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.37	377	309	1.22	0.0000181	3268
Missense in Polyphen		107	103.23	1.0365		1060
Synonymous	-3.61	193	139	1.39	0.00000915	1059
Loss of Function	0.434	19	21.2	0.898	9.32e-7	227

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000157	0.000157
Ashkenazi Jewish	0.00	0.00
East Asian	0.000579	0.000544
Finnish	0.0000477	0.0000462
European (Non-Finnish)	0.000172	0.000167
Middle Eastern	0.000579	0.000544
South Asian	0.000132	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the second step in the formation of the mannose 6-phosphate targeting signal on lysosomal enzyme oligosaccharides by removing GlcNAc residues from GlcNAc-alpha-P- mannose moieties, which are formed in the first step. Also hydrolyzes UDP-GlcNAc, a sugar donor for Golgi N- acetylglucosaminyltransferases. {ECO:0000269|PubMed:23572527}.;
Disease: DISEASE: Note=Defects in NAGPA have been suggested to play a role in susceptibility to persistent stuttering. Stuttering is a common speech disorder characterized by repetitions, prolongations, and interruptions in the flow of speech. {ECO:0000269|PubMed:20147709}.;
Pathway: Lysosome - Homo sapiens (human) (Consensus)

Recessive Scores

pRec: 0.274

Intolerance Scores

loftool: 0.575
rvis_EVS: 0
rvis_percentile_EVS: 54.03

Haploinsufficiency Scores

pHI: 0.0906
hipred: N
hipred_score: 0.396
ghis: 0.515

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.941

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Nagpa
Phenotype: cellular phenotype;

Gene ontology

Biological process: carbohydrate metabolic process;cellular protein modification process;protein glycosylation;protein targeting to lysosome;lysosome organization;secretion of lysosomal enzymes
Cellular component: integral component of membrane;Golgi cisterna membrane
Molecular function: N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase activity;protein binding