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.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				10	5	15
missense			44	6	3	53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	2	3
Total	0	0	44	17	10

Variants in NAGPA

This is a list of pathogenic ClinVar variants found in the NAGPA region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
16-5025472-GAGGCTTCAGTCCTTGA-G		Variant of unknown significance	Uncertain significance (Nov 18, 2011)
16-5025483-C-A		not specified	Uncertain significance (Aug 09, 2021)
16-5025492-G-T		not specified	Uncertain significance (Jan 08, 2024)
16-5025493-G-A		NAGPA-related disorder	Likely benign (Feb 22, 2019)
16-5025513-G-T		not specified	Uncertain significance (Aug 21, 2023)
16-5025525-C-T		NAGPA-related disorder	Benign (Apr 29, 2019)
16-5025536-T-G		not specified	Uncertain significance (May 11, 2022)
16-5025541-G-A		not specified	Benign (-)
16-5025550-C-T		NAGPA-related disorder	Likely benign (Aug 12, 2019)
16-5025551-T-C		not specified	Uncertain significance (Jun 17, 2024)
16-5025569-T-G		not specified	Uncertain significance (Jun 03, 2022)
16-5025587-C-T		not specified	Uncertain significance (Feb 22, 2023)
16-5025597-C-T		not specified	Uncertain significance (May 09, 2023)
16-5025632-G-A		not specified	Benign (-)
16-5027156-C-G		NAGPA-related disorder	Likely benign (Apr 25, 2023)
16-5027181-G-T		not specified	Uncertain significance (Apr 12, 2022)
16-5027186-A-G		not specified	Uncertain significance (Jul 25, 2023)
16-5027287-C-T		not specified	Likely benign (Dec 06, 2021)
16-5027288-G-A		NAGPA-related disorder	Likely benign (Aug 12, 2019)
16-5027351-G-C			Benign/Likely benign (Oct 01, 2024)
16-5027374-G-A		not specified	Uncertain significance (Nov 13, 2023)
16-5027394-TGGGAGGA-T		not specified	Likely benign (-)
16-5027874-G-A			Likely benign (Dec 01, 2022)
16-5027983-C-T		not specified	Uncertain significance (Jun 16, 2023)
16-5027984-C-T			Benign (Dec 31, 2019)

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