NAPG

NSF attachment protein gamma

Basic information

Region (hg38): 18:10525904-10552764

Links

ENSG00000134265 ∙ NCBI:8774 ∙ OMIM:603216 ∙ HGNC:7642 ∙ Uniprot:Q99747 ∙ 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 NAPG gene.

• Inborn genetic diseases (9 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAPG 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						0
missense			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in NAPG

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

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

Position	Type	Phenotype	Significance	ClinVar
18-10532788-A-G		not specified	Uncertain significance (Dec 19, 2022)
18-10533538-T-G		not specified	Uncertain significance (Jun 11, 2021)
18-10539786-G-A		not specified	Uncertain significance (Mar 01, 2023)
18-10539835-C-A		not specified	Uncertain significance (Jun 29, 2023)
18-10539852-G-A		not specified	Uncertain significance (Jun 30, 2022)
18-10540046-G-C		not specified	Uncertain significance (Feb 13, 2024)
18-10540345-G-A		not specified	Uncertain significance (Sep 14, 2022)
18-10540390-G-A		not specified	Uncertain significance (Jun 03, 2022)
18-10546337-C-T		not specified	Uncertain significance (Aug 15, 2023)
18-10546357-GAAA-G			Uncertain significance (Mar 01, 2023)
18-10548308-G-A		not specified	Uncertain significance (Nov 17, 2023)
18-10549065-A-G		not specified	Uncertain significance (Feb 13, 2024)
18-10550210-G-A		not specified	Uncertain significance (Jul 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAPG	protein_coding	protein_coding	ENST00000322897	12	26857

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0812	0.918	124626	0	12	124638	0.0000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.569	135	155	0.871	0.00000773	2002
Missense in Polyphen		31	43.652	0.71016		533
Synonymous	0.355	52	55.4	0.939	0.00000279	563
Loss of Function	3.10	6	21.5	0.279	0.00000127	259

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000558	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000551	0.0000531
Middle Eastern	0.0000558	0.0000556
South Asian	0.000139	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for vesicular transport between the endoplasmic reticulum and the Golgi apparatus.
• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;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: 0.127

Intolerance Scores

• loftool: 0.620
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.426
• ghis: 0.648

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.747

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Napg

Gene ontology

• Biological process: intracellular protein transport;intra-Golgi vesicle-mediated transport;protein stabilization;membrane fusion;protein-containing complex assembly
• Cellular component: mitochondrion;lysosomal membrane;vacuolar membrane;SNARE complex;myelin sheath;synapse;extracellular exosome
• Molecular function: soluble NSF attachment protein activity;protein binding;syntaxin binding