NAPA

NSF attachment protein alpha

Basic information

Region (hg38): 19:47487637-47515091

Links

ENSG00000105402 ∙ NCBI:8775 ∙ OMIM:603215 ∙ HGNC:7641 ∙ Uniprot:P54920 ∙ 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 NAPA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAPA 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				1		1
missense			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in NAPA

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

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

Position	Type	Phenotype	Significance	ClinVar
19-47488299-C-T		not specified	Uncertain significance (Mar 06, 2025)
19-47488343-G-A		not specified	Uncertain significance (Oct 04, 2024)
19-47488364-C-T		not specified	Uncertain significance (Dec 09, 2023)
19-47490808-G-A		not specified	Uncertain significance (Jan 03, 2024)
19-47490820-A-G		not specified	Uncertain significance (Dec 13, 2022)
19-47492052-G-C		not specified	Uncertain significance (Dec 10, 2024)
19-47492063-G-T		not specified	Uncertain significance (May 27, 2022)
19-47492073-T-C		not specified	Uncertain significance (Jul 20, 2021)
19-47492077-C-T		not specified	Uncertain significance (Mar 03, 2025)
19-47492089-G-A		not specified	Uncertain significance (Nov 16, 2024)
19-47492098-T-G		not specified	Uncertain significance (Aug 08, 2022)
19-47492101-C-T		not specified	Uncertain significance (Jan 29, 2025)
19-47493008-C-T		not specified	Uncertain significance (Aug 04, 2023)
19-47493448-T-G		not specified	Uncertain significance (Aug 28, 2024)
19-47493465-T-C		not specified	Uncertain significance (Sep 22, 2023)
19-47493489-C-T		not specified	Uncertain significance (Oct 03, 2024)
19-47495551-A-G		not specified	Uncertain significance (Dec 20, 2023)
19-47495560-T-C		not specified	Uncertain significance (Oct 17, 2023)
19-47495570-T-C		not specified	Uncertain significance (Dec 19, 2022)
19-47500642-C-T		not specified	Uncertain significance (Jul 27, 2024)
19-47500657-C-T		not specified	Uncertain significance (Dec 20, 2023)
19-47500667-G-A			Likely benign (Mar 01, 2023)
19-47500726-C-A		not specified	Uncertain significance (Apr 20, 2023)
19-47500738-C-T		not specified	Uncertain significance (Dec 06, 2022)
19-47503450-T-C		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAPA	protein_coding	protein_coding	ENST00000263354	11	27604

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.240	0.760	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.993	142	179	0.791	0.0000105	1957
Missense in Polyphen		34	47.814	0.71109		513
Synonymous	-0.347	81	77.1	1.05	0.00000567	514
Loss of Function	3.17	5	20.5	0.244	9.56e-7	237

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000619	0.0000615
Middle Eastern	0.000109	0.000109
South Asian	0.000170	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for vesicular transport between the endoplasmic reticulum and the Golgi apparatus (Probable). Together with GNA12 promotes CDH5 localization to plasma membrane (PubMed:15980433). {ECO:0000269|PubMed:15980433, ECO:0000305}.
• Pathway: Synaptic vesicle cycle - Homo sapiens (human);Synaptic Vesicle Pathway;Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Intra-Golgi traffic;COPI-mediated anterograde transport;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.412
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.528
• hipred: Y
• hipred_score: 0.739
• ghis: 0.569

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.971

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Napa
• Phenotype: craniofacial phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;intra-Golgi vesicle-mediated transport;brain development;regulation of synaptic vesicle priming;synaptic vesicle priming;neuron differentiation;positive regulation of ATPase activity;synaptic transmission, glutamatergic;SNARE complex disassembly;apical protein localization;COPII vesicle coating;membrane fusion
• Cellular component: Golgi membrane;vacuolar membrane;cytosol;plasma membrane;membrane;SNARE complex;myelin sheath;synaptobrevin 2-SNAP-25-syntaxin-1a complex;extracellular exosome;presynapse;postsynapse;glutamatergic synapse
• Molecular function: SNARE binding;soluble NSF attachment protein activity;protein binding;syntaxin binding;protein-containing complex binding