NAV1

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

Basic information

Region (hg38): 1:201539126-201826969

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.

• Inborn genetic diseases (50 variants)
• not provided (16 variants)
• not specified (1 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.

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				1	9	10
missense			47	3	3	53
nonsense				1		1
start loss						0
frameshift			1			1
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	48	6	12

Variants in NAV1

This is a list of pathogenic ClinVar variants found in the NAV1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-201648717-A-G		not specified	Uncertain significance (Apr 07, 2023)
1-201648720-G-A		not specified	Uncertain significance (Apr 07, 2023)
1-201648725-C-A			Benign (Apr 04, 2018)
1-201648756-G-T		not specified	Uncertain significance (Jan 03, 2024)
1-201648808-C-G		not specified	Uncertain significance (Feb 10, 2022)
1-201648817-CCGGCGG-C			Likely benign (Nov 01, 2021)
1-201648869-C-G		not specified	Uncertain significance (Nov 17, 2022)
1-201648888-A-G		not specified	Likely benign (Apr 07, 2023)
1-201648912-G-A			Benign (May 15, 2018)
1-201648916-C-T		not specified	Uncertain significance (Jan 03, 2024)
1-201649030-G-T		not specified	Uncertain significance (Oct 13, 2023)
1-201649129-C-T		not specified	Uncertain significance (Nov 27, 2023)
1-201649136-C-T			Benign (Jun 17, 2020)
1-201649324-C-A		not specified	Uncertain significance (Oct 26, 2022)
1-201718439-G-A		not specified	Uncertain significance (Jan 23, 2024)
1-201718479-G-A		not specified	Uncertain significance (May 17, 2023)
1-201718508-G-T		not specified	Uncertain significance (Apr 13, 2023)
1-201718518-C-T		not specified	Uncertain significance (Jul 13, 2022)
1-201718545-C-T		not specified	Uncertain significance (Aug 21, 2023)
1-201718574-G-A		not specified	Uncertain significance (Dec 21, 2021)
1-201718611-G-A		not specified	Uncertain significance (Nov 12, 2021)
1-201718686-A-G		not specified	Uncertain significance (Feb 15, 2023)
1-201718698-T-C		not specified	Uncertain significance (Sep 29, 2023)
1-201780563-C-T			Likely benign (Jul 01, 2023)
1-201781012-C-G		not specified	Uncertain significance (Sep 29, 2022)

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