NAV3 neuron navigator 3 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

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_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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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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 EBI GWAS CatalogPubMed
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 EBI GWAS CatalogPubMed
Genome-wide and candidate gene association study of cigarette smoking behaviors. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of ancestry-specific TB risk in the South African Coloured population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D12S2006 (e-PCR)
- UniSTS:1819

G62498 (e-PCR)
- UniSTS:139556

D19S653E (e-PCR)
- UniSTS:150568

SHGC-154971 (e-PCR)
- UniSTS:182600

SHGC-155034 (e-PCR)
- UniSTS:182603

RH46017 (e-PCR)
- UniSTS:31332

RH103582 (e-PCR)
- UniSTS:97907

SHGC-79622 (e-PCR)
- UniSTS:182653

D12S1376E (e-PCR)
- UniSTS:153777

L17987 (e-PCR)
- UniSTS:53723

D12S277E (e-PCR)
- UniSTS:473053

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)

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
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

NC_000012.12 Reference GRCh38.p14 Primary Assembly

Range

77571862..78213010

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017020166.3 → XP_016875655.1 neuron navigator 3 isoform X9
XM_047429817.1 → XP_047285773.1 neuron navigator 3 isoform X13
XM_047429823.1 → XP_047285779.1 neuron navigator 3 isoform X22
XM_017020167.1 → XP_016875656.1 neuron navigator 3 isoform X12
XM_047429818.1 → XP_047285774.1 neuron navigator 3 isoform X14
XM_047429819.1 → XP_047285775.1 neuron navigator 3 isoform X15
XM_047429826.1 → XP_047285782.1 neuron navigator 3 isoform X25
XM_017020164.3 → XP_016875653.1 neuron navigator 3 isoform X1
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
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
XM_017020165.2 → XP_016875654.1 neuron navigator 3 isoform X2
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
XM_017020168.2 → XP_016875657.1 neuron navigator 3 isoform X16
XM_047429820.1 → XP_047285776.1 neuron navigator 3 isoform X18
XM_017020169.3 → XP_016875658.1 neuron navigator 3 isoform X17
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
XM_017020170.2 → XP_016875659.1 neuron navigator 3 isoform X20
XM_047429813.1 → XP_047285769.1 neuron navigator 3 isoform X7
XM_047429812.1 → XP_047285768.1 neuron navigator 3 isoform X4
XM_047429814.1 → XP_047285770.1 neuron navigator 3 isoform X8
XM_047429815.1 → XP_047285771.1 neuron navigator 3 isoform X10
XM_047429816.1 → XP_047285772.1 neuron navigator 3 isoform X11
XM_047429822.1 → XP_047285778.1 neuron navigator 3 isoform X21
XM_047429824.1 → XP_047285780.1 neuron navigator 3 isoform X23
XM_047429825.1 → XP_047285781.1 neuron navigator 3 isoform X24
XM_017020171.2 → XP_016875660.1 neuron navigator 3 isoform X26
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)
XM_017020173.3 → XP_016875662.1 neuron navigator 3 isoform X28
XM_017020175.2 → XP_016875664.1 neuron navigator 3 isoform X29