NAV2

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

Basic information

Region (hg38): 11:19350723-20121601

Links

ENSG00000166833 ∙ NCBI:89797 ∙ OMIM:607026 ∙ HGNC:15997 ∙ Uniprot:Q8IVL1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NAV2 gene.

• Inborn genetic diseases (105 variants)
• not provided (35 variants)
• NAV2-related condition (4 variants)
• NAV2-related neurodevelopmental condition (2 variants)
• Hirschsprung disease, susceptibility to, 1 (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAV2 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				5	9	14
missense			118	2	1	121
nonsense			2			2
start loss						0
frameshift			2			2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	2	4
non coding					1	1
Total	0	0	122	7	11

Variants in NAV2

This is a list of pathogenic ClinVar variants found in the NAV2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-19713721-A-C			Uncertain significance (Nov 10, 2023)
11-19713726-A-G		not specified	Uncertain significance (Feb 28, 2024)
11-19713734-A-C		NAV2-related disorder	Likely benign (Feb 01, 2024)
11-19713746-C-G		NAV2-related disorder	Benign (Jan 13, 2020)
11-19713747-G-A		not specified	Uncertain significance (Jun 07, 2023)
11-19713779-C-A		NAV2-related disorder	Benign (Jan 03, 2020)
11-19713802-C-A		not specified	Uncertain significance (Feb 27, 2023)
11-19713823-G-A		not specified	Uncertain significance (Dec 18, 2023)
11-19713846-A-T		not specified	Uncertain significance (Nov 02, 2023)
11-19713850-A-G		NAV2-related disorder	Likely benign (Feb 20, 2023)
11-19713865-C-G		NAV2-related disorder	Benign (Nov 25, 2019)
11-19713892-T-A		not specified	Uncertain significance (Feb 26, 2024)
11-19832542-G-A		NAV2-related disorder	Benign (Oct 30, 2019)
11-19832549-C-T		NAV2-related disorder	Benign/Likely benign (May 01, 2022)
11-19842881-G-T		NAV2-related disorder	Uncertain significance (Oct 24, 2022)
11-19868958-G-T		not specified	Uncertain significance (Feb 07, 2023)
11-19868983-G-A		not specified	Uncertain significance (Sep 01, 2021)
11-19879976-C-T		not specified	Uncertain significance (Aug 08, 2023)
11-19879982-G-A		not specified	Uncertain significance (Nov 07, 2023)
11-19880000-G-A		not specified	Uncertain significance (Sep 13, 2022)
11-19880003-G-A		not specified	Uncertain significance (Dec 19, 2023)
11-19880004-C-G		not specified	Uncertain significance (Feb 28, 2024)
11-19880028-C-T		NAV2-related disorder	Uncertain significance (Jun 12, 2023)
11-19880031-C-T		not specified	Uncertain significance (Jun 21, 2022)
11-19880042-G-T		not specified	Uncertain significance (Jan 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAV2	protein_coding	protein_coding	ENST00000396087	41	770874

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000454	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	1314	1.46e+3	0.898	0.0000888	16251
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000211	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000134	0.000132
Middle Eastern	0.000272	0.000272
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.416
• hipred: Y
• hipred_score: 0.554
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.857

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nav2
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; taste/olfaction phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); vision/eye phenotype

Gene ontology

• Biological process: regulation of systemic arterial blood pressure by baroreceptor feedback;nervous system development;sensory perception of sound;sensory perception of smell;locomotory behavior;optic nerve development;glossopharyngeal nerve development;vagus nerve development;neurogenesis
• Cellular component: interstitial matrix;nucleoplasm
• Molecular function: helicase activity;protein binding;ATP binding;heparin binding