NAPB

NSF attachment protein beta

Basic information

Region (hg38): 20:23374518-23421519

Links

ENSG00000125814 ∙ NCBI:63908 ∙ OMIM:611270 ∙ HGNC:15751 ∙ Uniprot:Q9H115 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• developmental and epileptic encephalopathy 107 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 107	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	26235277; 28097321; 33189936

ClinVar

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

• Inborn genetic diseases (10 variants)
• Developmental and epileptic encephalopathy-107 (3 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAPB 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			8		1	9
nonsense	2					2
start loss			2			2
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			1			1
Total	2	0	11	0	1

Variants in NAPB

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

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

Position	Type	Phenotype	Significance	ClinVar
20-23379443-A-G		Malignant tumor of prostate	Uncertain significance (-)
20-23379446-G-A		Inborn genetic diseases	Uncertain significance (Aug 10, 2023)
20-23379880-C-T		Inborn genetic diseases	Uncertain significance (Apr 25, 2023)
20-23381237-G-T		Inborn genetic diseases	Uncertain significance (Feb 11, 2022)
20-23381263-A-G		Inborn genetic diseases	Uncertain significance (Sep 16, 2021)
20-23381302-T-C		Inborn genetic diseases	Uncertain significance (Jun 06, 2023)
20-23390028-G-T		Developmental and epileptic encephalopathy-107	Pathogenic (Sep 13, 2022)
20-23390261-T-C		Inborn genetic diseases	Uncertain significance (Oct 03, 2022)
20-23390265-C-T		Developmental and epileptic encephalopathy, 1 • Developmental and epileptic encephalopathy-107	Conflicting classifications of pathogenicity (Sep 13, 2022)
20-23394969-T-C		Inborn genetic diseases	Uncertain significance (Dec 20, 2023)
20-23395141-T-C		Inborn genetic diseases	Uncertain significance (Dec 09, 2023)
20-23395148-G-T		Developmental and epileptic encephalopathy-107	Pathogenic (-)
20-23395193-G-A			Likely benign (Aug 01, 2022)
20-23397131-T-C		Inborn genetic diseases	Uncertain significance (Jun 29, 2021)
20-23402998-C-T		Developmental and epileptic encephalopathy-107	Pathogenic (May 08, 2023)
20-23403046-C-T		Inborn genetic diseases	Uncertain significance (Jun 11, 2021)
20-23421334-G-A		NAPB-related disorder	Likely benign (Nov 14, 2019)
20-23421338-T-C		NAPB-related disorder	Benign (Sep 30, 2019)
20-23421351-C-T		Inborn genetic diseases	Uncertain significance (Nov 30, 2022)
20-23421392-G-C		Inborn genetic diseases	Uncertain significance (Aug 10, 2021)
20-23421401-A-C		Developmental and epileptic encephalopathy-107	Uncertain significance (Nov 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAPB	protein_coding	protein_coding	ENST00000377026	11	46967

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.112	0.887	125720	0	7	125727	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	95	150	0.632	0.00000681	1975
Missense in Polyphen		34	56.605	0.60065		744
Synonymous	0.598	45	50.4	0.893	0.00000237	502
Loss of Function	2.85	5	18.1	0.277	7.63e-7	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000292	0.0000292
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000451	0.0000440
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for vesicular transport between the endoplasmic reticulum and the Golgi apparatus. {ECO:0000250}.
• Pathway: 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: 0.136

Intolerance Scores

• loftool: 0.292
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.314
• hipred: Y
• hipred_score: 0.673
• ghis: 0.636

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.581

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Napb
• 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: napbb
• Affected structure: horizontal cell
• Phenotype tag: abnormal
• Phenotype quality: absent

Gene ontology

• Biological process: intracellular protein transport;regulation of synaptic vesicle priming;synaptic transmission, glutamatergic;SNARE complex disassembly
• Cellular component: vacuolar membrane;SNARE complex;synaptobrevin 2-SNAP-25-syntaxin-1a complex;extracellular exosome
• Molecular function: soluble NSF attachment protein activity;protein binding;syntaxin binding