NAV2

protein-coding

neuron navigator 2, the group of MicroRNA protein coding host genes

Gene summary

This gene encodes a member of the neuron navigator gene family, which may play a role in cellular growth and migration. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

MANE transcript

NM_145117.5

Inheritance

ClinVar variants

U:413B:47

Top phenotype

NAV2-related disorder

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr11:19,350,724-20,121,601

External References & Databases

Ensembl (ENSG00000166833)

Transcript & Mutation Effects

hg38 • Region Span ~770.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NAV2 variants in ClinVar

7 Conditions Cataloged

not specifiedTotal: 380

NAV2-related disorderTotal: 45

not providedTotal: 34

NAV2-related neurodevelopmental conditionTotal: 2

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

Hirschsprung disease, susceptibility to, 1Total: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145117.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			6 clinvar	17 clinvar	9 clinvar	32
missense			391 clinvar	16 clinvar	5 clinvar	412
nonsense			4 clinvar			4
start loss						0
frameshift			3 clinvar			3
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	413	33	14	460

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 65 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145117.5	RefSeq	NP_660093.2	38	MANE Select
ENST00000349880.9	Ensembl	ENSP00000309577.6	38	MANE Select
NM_001111018.2	RefSeq	NP_001104488.1	38	Standard
NM_001111019.3	RefSeq	NP_001104489.1	27	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of systemic arterial blood pressure by baroreceptor feedback
nervous system development
sensory perception of sound
sensory perception of smell
locomotory behavior

Molecular Function

helicase activity
protein binding
ATP binding
heparin binding

Cellular Component

interstitial matrix
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396087
Coding exons: 41
Length: 770874
Individuals with no LoFs: 125720
Homozygous LoFs: 0
Heterozygous LoFs: 28
Defined: 125748
p: 0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.39	1314	1.46e+3	0.898	0.0000888	16251
Missense (PolyPhen)		703	862.58	0.815		9622
Synonymous	-1.07	629	596	1.06	0.0000386	5045
Loss of Function	7.87	17	103	0.165	0.00000498	1246

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00013	0.00013	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Possesses 3' to 5' helicase activity and exonuclease activity. Involved in neuronal development, specifically in the development of different sensory organs. {ECO:0000269|PubMed:12214280, ECO:0000269|PubMed:15158073}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.373
RVIS EVS: -1.56
RVIS percentile EVS: 3.22

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.857

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High