NAV1

neuron navigator 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 1:201539127-201826969

Links

ENSG00000134369 ∙ NCBI:89796 ∙ OMIM:611628 ∙ HGNC:15989 ∙ Uniprot:Q8NEY1 ∙ 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 NAV1 gene.

• not_specified (171 variants)
• not_provided (15 variants)
• Autism_spectrum_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NAV1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001389617.1. 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				2	9	11
missense			164	5	3	172
nonsense				1		1
start loss						0
frameshift			1			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	165	8	12

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NAV1	protein_coding	protein_coding	ENST00000367296	30	203692

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	8.00e-12	125728	0	3	125731	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.15	708	1.09e+3	0.647	0.0000637	12169
Missense in Polyphen		234	461.89	0.50662		5083
Synonymous	0.772	426	447	0.954	0.0000260	3924
Loss of Function	8.01	2	78.7	0.0254	0.00000412	933

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000267	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in neuronal migration. {ECO:0000250}.

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.00138
• rvis_EVS: -1.6
• rvis_percentile_EVS: 3.01

Haploinsufficiency Scores

• pHI: 0.181
• hipred: Y
• hipred_score: 0.774
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.848

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nav1

Gene ontology

• Biological process: microtubule bundle formation;neuron migration;nervous system development
• Cellular component: cytoplasm;microtubule;microtubule cytoskeleton;axon initial segment