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NAV3 neuron navigator 3 [ Homo sapiens (human) ]

Gene ID: 89795, updated on 3-Nov-2024

Summary

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Official Symbol
NAV3provided by HGNC
Official Full Name
neuron navigator 3provided by HGNC
Primary source
HGNC:HGNC:15998
See related
Ensembl:ENSG00000067798 MIM:611629; AllianceGenome:HGNC:15998
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
POMFIL1; unc53H3; STEERIN3
Summary
This gene belongs to the neuron navigator family and is expressed predominantly in the nervous system. The encoded protein contains coiled-coil domains and a conserved AAA domain characteristic for ATPases associated with a variety of cellular activities. This gene is similar to unc-53, a Caenorhabditis elegans gene involved in axon guidance. Multiple alternatively spliced transcript variants for this gene have been described but only one has had its full-length nature determined. [provided by RefSeq, Jul 2008]
Expression
Broad expression in brain (RPKM 3.5), ovary (RPKM 2.8) and 14 other tissues See more
Orthologs
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Genomic context

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See NAV3 in Genome Data Viewer
Location:
12q21.2
Exon count:
42
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (77571862..78213010)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (77549793..78191344)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (78224674..78606790)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:77631785-77632286 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:77633489-77633990 Neighboring gene long intergenic non-protein coding RNA 2464 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4678 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:77741435-77742634 Neighboring gene uncharacterized LOC124902972 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr12:78038694-78039502 Neighboring gene NANOG hESC enhancer GRCh37_chr12:78039827-78040389 Neighboring gene Sharpr-MPRA regulatory region 9790 Neighboring gene Sharpr-MPRA regulatory region 15641 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:78282205-78283404 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:78333298-78334497 Neighboring gene NANOG hESC enhancer GRCh37_chr12:78375957-78376518 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:78495967-78496468 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:78496469-78496968 Neighboring gene peroxiredoxin like 2A pseudogene 1 Neighboring gene uncharacterized LOC105369859 Neighboring gene long intergenic non-protein coding RNA 2424 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4679 Neighboring gene mitochondrial ribosomal protein L11 pseudogene 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Clinicopathological characterization and genomic aberrations in subcutaneous panniculitis-like T-cell lymphoma. Hahtola S, et al. J Invest Dermatol, 2008 Sep. PMID 18337827
  2. Primary cutaneous T-cell lymphomas do not show specific NAV3 gene deletion or translocation. Marty M, et al. J Invest Dermatol, 2008 Oct. PMID 18509363
  3. Cutaneous-type adult T-cell leukemia/lymphoma does not primarily show deletion of NAV3 gene. Kawai K, et al. J Invest Dermatol, 2010 Jan. PMID 19626031
  4. NAV3 copy number changes and target genes in basal and squamous cell cancers. Maliniemi P, et al. Exp Dermatol, 2011 Nov. PMID 21995814
  5. Potential role of a navigator gene NAV3 in colorectal cancer. Carlsson E, et al. Br J Cancer, 2012 Jan 31. PMID 22173670, Free PMC Article

See all (40) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Mutated neuron navigator 3 as a candidate gene for a rare neurodevelopmental disorder.
    Title: Mutated neuron navigator 3 as a candidate gene for a rare neurodevelopmental disorder.
  2. Variants of NAV3, a neuronal morphogenesis protein, cause intellectual disability, developmental delay, and microcephaly.
    Title: Variants of NAV3, a neuronal morphogenesis protein, cause intellectual disability, developmental delay, and microcephaly.
  3. Tumour Suppressor Neuron Navigator 3 and Matrix Metalloproteinase 14 are Co-expressed in Most Melanomas but Downregulated in Thick Tumours.
    Title: Tumour Suppressor Neuron Navigator 3 and Matrix Metalloproteinase 14 are Co-expressed in Most Melanomas but Downregulated in Thick Tumours.
  4. Together, our findings suggest an important role for miR-21 in the progression of HCC, which negatively regulated Navigator-3 in the migration of HCC.
    Title: MiR-21 promoted proliferation and migration in hepatocellular carcinoma through negative regulation of Navigator-3.
  5. The authers propose that NAV3 inhibits breast cancer progression by regulating microtubule dynamics, biasing directionally persistent rather than random migration, and inhibiting locomotion of initiated cells.
    Title: Navigator-3, a modulator of cell migration, may act as a suppressor of breast cancer progression.
  6. Data indicate that neuron navigator 3 (NAV3) may be a potential new prognostic biomarker and a potential therapeutic target.
    Title: Neuron navigator 3 alterations in nervous system tumors associate with tumor malignancy grade and prognosis.
  7. NAV3 has a role in linking tissue inflammation to cancer development in the colon.
    Title: Potential role of a navigator gene NAV3 in colorectal cancer.
  8. characterized copy number changes of NAV3 in 24 basal cell cancers, eight squamous cell cancers and eight non-malignant inflammatory skin lesions
    Title: NAV3 copy number changes and target genes in basal and squamous cell cancers.
  9. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  10. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
Submit: New GeneRIF Correction See all GeneRIFs (14)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study of self-rated health.
EBI GWAS Catalog
A genome-wide association study provides evidence for association of chromosome 8p23 (MYP10) and 10q21.1 (MYP15) with high myopia in the French Population.
EBI GWAS Catalog
Genome-wide and candidate gene association study of cigarette smoking behaviors.
EBI GWAS Catalog
Genome-wide association study of ancestry-specific TB risk in the South African Coloured population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0938

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables ATP hydrolysis activity IEA
Inferred from Electronic Annotation
more info
  
enables microtubule binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of cell migration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of interleukin-2 production IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of microtubule depolymerization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neurogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of microtubule polymerization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
colocalizes_with microtubule end IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in nuclear outer membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
neuron navigator 3
Names
pore membrane and/or filament interacting like protein 1
unc-53 homolog 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001024383.2 → NP_001019554.1  neuron navigator 3 isoform 1

    See identical proteins and their annotated locations for NP_001019554.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AB023155, AC073571, AC073608, AC138331, AJ488201, AV728995, DR005268
    Consensus CDS
    CCDS66432.1
    UniProtKB/Swiss-Prot
    Q8IVL0, Q8NFW7, Q9Y2E7
    Related
    ENSP00000381007.2, ENST00000397909.7
    Conserved Domains (6) summary
    cd00009
    Location:2052 → 2132
    AAA; The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, ...
    smart00382
    Location:2049 → 2169
    AAA; ATPases associated with a variety of cellular activities
    cd00014
    Location:81 → 182
    CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...
    pfam15898
    Location:1794 → 1857
    PRKG1_interact; cGMP-dependent protein kinase interacting domain
    cl11266
    Location:468 → 545
    EssA; WXG100 protein secretion system (Wss), protein EssA
    cl21455
    Location:2036 → 2066
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  2. NM_014903.6 → NP_055718.4  neuron navigator 3 isoform 2

    See identical proteins and their annotated locations for NP_055718.4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC073571, AC073608, AC138331, AJ488201
    Consensus CDS
    CCDS41815.1
    UniProtKB/Swiss-Prot
    Q8IVL0
    Related
    ENSP00000446132.2, ENST00000536525.6
    Conserved Domains (6) summary
    cd00009
    Location:2030 → 2110
    AAA; The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, ...
    smart00382
    Location:2027 → 2147
    AAA; ATPases associated with a variety of cellular activities
    cd00014
    Location:81 → 182
    CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...
    pfam15898
    Location:1772 → 1835
    PRKG1_interact; cGMP-dependent protein kinase interacting domain
    cl11266
    Location:468 → 545
    EssA; WXG100 protein secretion system (Wss), protein EssA
    cl21455
    Location:2014 → 2044
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    77571862..78213010
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017020166.3 → XP_016875655.1  neuron navigator 3 isoform X9

  2. XM_047429817.1 → XP_047285773.1  neuron navigator 3 isoform X13

  3. XM_047429823.1 → XP_047285779.1  neuron navigator 3 isoform X22

  4. XM_017020167.1 → XP_016875656.1  neuron navigator 3 isoform X12

  5. XM_047429818.1 → XP_047285774.1  neuron navigator 3 isoform X14

  6. XM_047429819.1 → XP_047285775.1  neuron navigator 3 isoform X15

  7. XM_047429826.1 → XP_047285782.1  neuron navigator 3 isoform X25

  8. XM_017020164.3 → XP_016875653.1  neuron navigator 3 isoform X1

  9. XM_005269215.5 → XP_005269272.1  neuron navigator 3 isoform X3

    Conserved Domains (6) summary
    cd00009
    Location:2023 → 2103
    AAA; The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, ...
    smart00382
    Location:2020 → 2140
    AAA; ATPases associated with a variety of cellular activities
    cd00014
    Location:81 → 182
    CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...
    pfam15898
    Location:1765 → 1828
    PRKG1_interact; cGMP-dependent protein kinase interacting domain
    cl11266
    Location:468 → 545
    EssA; WXG100 protein secretion system (Wss), protein EssA
    cl21455
    Location:2007 → 2037
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  10. XM_011538940.3 → XP_011537242.1  neuron navigator 3 isoform X5

    Conserved Domains (6) summary
    cd00009
    Location:2016 → 2096
    AAA; The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, ...
    smart00382
    Location:2013 → 2133
    AAA; ATPases associated with a variety of cellular activities
    cd00014
    Location:81 → 182
    CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...
    pfam15898
    Location:1758 → 1821
    PRKG1_interact; cGMP-dependent protein kinase interacting domain
    cl11266
    Location:468 → 545
    EssA; WXG100 protein secretion system (Wss), protein EssA
    cl21455
    Location:2000 → 2030
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  11. XM_017020165.2 → XP_016875654.1  neuron navigator 3 isoform X2

  12. XM_011538941.3 → XP_011537243.1  neuron navigator 3 isoform X6

    Conserved Domains (6) summary
    cd00009
    Location:2009 → 2089
    AAA; The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, ...
    smart00382
    Location:2006 → 2126
    AAA; ATPases associated with a variety of cellular activities
    cd00014
    Location:81 → 182
    CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...
    pfam15898
    Location:1751 → 1814
    PRKG1_interact; cGMP-dependent protein kinase interacting domain
    cl11266
    Location:468 → 545
    EssA; WXG100 protein secretion system (Wss), protein EssA
    cl21455
    Location:1993 → 2023
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  13. XM_017020168.2 → XP_016875657.1  neuron navigator 3 isoform X16

  14. XM_047429820.1 → XP_047285776.1  neuron navigator 3 isoform X18

  15. XM_017020169.3 → XP_016875658.1  neuron navigator 3 isoform X17

  16. XM_011538944.4 → XP_011537246.1  neuron navigator 3 isoform X19

    UniProtKB/Swiss-Prot
    Q8IVL0
    Conserved Domains (6) summary
    cd00009
    Location:1853 → 1933
    AAA; The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, ...
    smart00382
    Location:1850 → 1970
    AAA; ATPases associated with a variety of cellular activities
    cd00014
    Location:81 → 182
    CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...
    pfam15898
    Location:1595 → 1658
    PRKG1_interact; cGMP-dependent protein kinase interacting domain
    cl11266
    Location:468 → 545
    EssA; WXG100 protein secretion system (Wss), protein EssA
    cl21455
    Location:1837 → 1867
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  17. XM_017020170.2 → XP_016875659.1  neuron navigator 3 isoform X20

  18. XM_047429813.1 → XP_047285769.1  neuron navigator 3 isoform X7

  19. XM_047429812.1 → XP_047285768.1  neuron navigator 3 isoform X4

  20. XM_047429814.1 → XP_047285770.1  neuron navigator 3 isoform X8

  21. XM_047429815.1 → XP_047285771.1  neuron navigator 3 isoform X10

  22. XM_047429816.1 → XP_047285772.1  neuron navigator 3 isoform X11

  23. XM_047429822.1 → XP_047285778.1  neuron navigator 3 isoform X21

  24. XM_047429824.1 → XP_047285780.1  neuron navigator 3 isoform X23

  25. XM_047429825.1 → XP_047285781.1  neuron navigator 3 isoform X24

  26. XM_017020171.2 → XP_016875660.1  neuron navigator 3 isoform X26

  27. XM_017020172.2 → XP_016875661.1  neuron navigator 3 isoform X27

    UniProtKB/TrEMBL
    A0A2R8YFX5
    Related
    ENSP00000495503.1, ENST00000644176.1
    Conserved Domains (3) summary
    smart00382
    Location:1506 → 1626
    AAA; ATPases associated with a variety of cellular activities
    PHA03307
    Location:469 → 793
    PHA03307; transcriptional regulator ICP4; Provisional
    pfam05109
    Location:657 → 937
    Herpes_BLLF1; Herpes virus major outer envelope glycoprotein (BLLF1)

  28. XM_017020173.3 → XP_016875662.1  neuron navigator 3 isoform X28

  29. XM_017020175.2 → XP_016875664.1  neuron navigator 3 isoform X29

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    77549793..78191344
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054373734.1 → XP_054229709.1  neuron navigator 3 isoform X9

  2. XM_054373738.1 → XP_054229713.1  neuron navigator 3 isoform X13

  3. XM_054373747.1 → XP_054229722.1  neuron navigator 3 isoform X22

  4. XM_054373737.1 → XP_054229712.1  neuron navigator 3 isoform X12

  5. XM_054373739.1 → XP_054229714.1  neuron navigator 3 isoform X14

  6. XM_054373740.1 → XP_054229715.1  neuron navigator 3 isoform X15

  7. XM_054373750.1 → XP_054229725.1  neuron navigator 3 isoform X25

  8. XM_054373726.1 → XP_054229701.1  neuron navigator 3 isoform X1

  9. XM_054373728.1 → XP_054229703.1  neuron navigator 3 isoform X3

  10. XM_054373730.1 → XP_054229705.1  neuron navigator 3 isoform X5

  11. XM_054373727.1 → XP_054229702.1  neuron navigator 3 isoform X2

  12. XM_054373731.1 → XP_054229706.1  neuron navigator 3 isoform X6

  13. XM_054373741.1 → XP_054229716.1  neuron navigator 3 isoform X16

  14. XM_054373743.1 → XP_054229718.1  neuron navigator 3 isoform X18

  15. XM_054373742.1 → XP_054229717.1  neuron navigator 3 isoform X17

  16. XM_054373744.1 → XP_054229719.1  neuron navigator 3 isoform X19

  17. XM_054373745.1 → XP_054229720.1  neuron navigator 3 isoform X20

  18. XM_054373732.1 → XP_054229707.1  neuron navigator 3 isoform X7

  19. XM_054373729.1 → XP_054229704.1  neuron navigator 3 isoform X4

  20. XM_054373733.1 → XP_054229708.1  neuron navigator 3 isoform X8

  21. XM_054373735.1 → XP_054229710.1  neuron navigator 3 isoform X10

  22. XM_054373736.1 → XP_054229711.1  neuron navigator 3 isoform X11

  23. XM_054373746.1 → XP_054229721.1  neuron navigator 3 isoform X21

  24. XM_054373748.1 → XP_054229723.1  neuron navigator 3 isoform X23

  25. XM_054373749.1 → XP_054229724.1  neuron navigator 3 isoform X24

  26. XM_054373751.1 → XP_054229726.1  neuron navigator 3 isoform X26

  27. XM_054373752.1 → XP_054229727.1  neuron navigator 3 isoform X27

    UniProtKB/TrEMBL
    A0A2R8YFX5

  28. XM_054373753.1 → XP_054229728.1  neuron navigator 3 isoform X28

  29. XM_054373754.1 → XP_054229729.1  neuron navigator 3 isoform X29

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IVL0.3 GenPept UniProtKB/Swiss-Prot:Q8IVL0

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