NAV3

neuron navigator 3

Basic information

Region (hg38): 12:77324641-78213010

Links

ENSG00000067798 ∙ NCBI:89795 ∙ OMIM:611629 ∙ HGNC:15998 ∙ Uniprot:Q8IVL0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder (Moderate), mode of inheritance: AD
• complex neurodevelopmental disorder (Definitive), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NAV3 gene.

• not_specified (237 variants)
• not_provided (26 variants)
• Neurodevelopmental_disorder_with_poor_or_absent_speech,_dysmorphic_facies,_and_behavioral_abnormalities (5 variants)
• Obesity (1 variants)
• NAV3-associated_neurodevelopmental_disorder (1 variants)
• Broad_eyebrow (1 variants)
• Midface_retrusion (1 variants)
• Sleep_apnea (1 variants)
• Hearing_impairment (1 variants)
• See_cases (1 variants)
• Cardiac_arrhythmia (1 variants)
• Trigonocephaly (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAV3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001024383.2. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	5	8
missense			245	4	2	251
nonsense	1	1	2			4
start loss						0
frameshift	1		1			2
splice donor/acceptor (+/-2bp)			1			1
Total	2	1	249	7	7

Highest pathogenic variant AF is 0.0000012419151

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAV3	protein_coding	protein_coding	ENST00000536525	39	382106

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	5.70e-9	124762	0	32	124794	0.000128

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	1127	1.26e+3	0.894	0.0000657	15393
Missense in Polyphen		449	561.81	0.7992		6929
Synonymous	-1.57	510	467	1.09	0.0000258	4723
Loss of Function	8.42	12	105	0.114	0.00000555	1321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000286	0.000284
Ashkenazi Jewish	0.00	0.00
East Asian	0.000115	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000115	0.000111
South Asian	0.000149	0.000131
Other	0.000663	0.000660

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate IL2 production by T-cells. May be involved in neuron regeneration. {ECO:0000269|PubMed:16166283}.
• Disease: DISEASE: Note=A chromosomal aberration disrupting NAV3 has been found in patients with Sezary syndrome (PubMed:16166283). Translocation t(12;18)(q21;q21.2) (PubMed:16166283). {ECO:0000269|PubMed:16166283}.
• Pathway: Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.228
• rvis_EVS: -2.05
• rvis_percentile_EVS: 1.65

Haploinsufficiency Scores

• pHI: 0.801
• hipred: Y
• hipred_score: 0.600
• ghis: 0.567

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.655

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nav3

Zebrafish Information Network

• Gene name: nav3
• Affected structure: liver primordium
• Phenotype tag: abnormal
• Phenotype quality: decreased size

Gene ontology

• Biological process: negative regulation of microtubule depolymerization;nervous system development;neurogenesis;negative regulation of cell migration;positive regulation of microtubule polymerization;negative regulation of interleukin-2 production;positive regulation of invadopodium disassembly
• Cellular component: nuclear outer membrane;microtubule end
• Molecular function: ATP binding;microtubule binding