NTNG1

netrin G1, the group of Netrins

Basic information

Region (hg38): 1:107140006-107484923

Links

ENSG00000162631 ∙ NCBI:22854 ∙ OMIM:608818 ∙ HGNC:23319 ∙ Uniprot:Q9Y2I2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• atypical Rett syndrome (Supportive), mode of inheritance: AD
• syndromic intellectual disability (Supportive), mode of inheritance: AD
• complex neurodevelopmental disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NTNG1 gene.

• not provided (18 variants)
• Inborn genetic diseases (12 variants)
• not specified (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 NTNG1 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	6	7
missense			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1		10	11
Total	0	0	14	1	16

Variants in NTNG1

This is a list of pathogenic ClinVar variants found in the NTNG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-107148301-A-G			Benign (Jun 20, 2021)
1-107148474-G-C			Benign (Jun 20, 2021)
1-107148668-G-A			Benign (Jun 05, 2018)
1-107149019-T-C			Benign (Jun 20, 2021)
1-107324330-C-G		not specified	Uncertain significance (May 30, 2023)
1-107324416-C-G		NTNG1-related disorder	Benign (Dec 16, 2019)
1-107324435-A-G		not specified	Uncertain significance (Jul 14, 2021)
1-107324443-G-A		NTNG1-related disorder	Benign/Likely benign (Apr 05, 2019)
1-107324465-C-T		NTNG1-related disorder	Benign (Sep 01, 2023)
1-107324617-G-C		not specified	Uncertain significance (Dec 07, 2021)
1-107324620-T-G		not specified	Uncertain significance (Sep 30, 2021)
1-107324669-A-C		not specified	Uncertain significance (Oct 02, 2023)
1-107324724-C-T			Uncertain significance (-)
1-107324830-G-T		not specified	Uncertain significance (Jan 03, 2024)
1-107324874-A-G		not specified	Uncertain significance (Sep 20, 2023)
1-107324876-T-C			Likely benign (Sep 01, 2023)
1-107324881-A-G			Benign (Jun 10, 2021)
1-107324896-G-A		NTNG1-related disorder	Likely benign (Dec 23, 2019)
1-107325019-C-T			Benign (Jun 19, 2021)
1-107325095-A-C			Benign (Jun 19, 2021)
1-107394846-C-G			Benign (Jun 20, 2021)
1-107395206-A-G		not specified	Uncertain significance (Apr 25, 2023)
1-107407690-A-G		not specified	Uncertain significance (Mar 11, 2022)
1-107418537-A-G			Benign (Jun 20, 2021)
1-107418574-G-A			Benign (Jun 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NTNG1	protein_coding	protein_coding	ENST00000370068	7	343452

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.917	0.0833	125650	0	26	125676	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.45	193	316	0.611	0.0000177	3530
Missense in Polyphen		59	134.75	0.43783		1547
Synonymous	0.429	125	131	0.952	0.00000861	1023
Loss of Function	3.96	4	25.6	0.156	0.00000143	297

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000166	0.000163
Finnish	0.000698	0.000693
European (Non-Finnish)	0.0000446	0.0000440
Middle Eastern	0.000166	0.000163
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in controlling patterning and neuronal circuit formation at the laminar, cellular, subcellular and synaptic levels. Promotes neurite outgrowth of both axons and dendrites. {ECO:0000269|PubMed:21946559}.
• Pathway: Cell adhesion molecules (CAMs) - Homo sapiens (human);Axon guidance - Homo sapiens (human);Splicing factor NOVA regulated synaptic proteins;Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.268
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.62

Haploinsufficiency Scores

• pHI: 0.0519
• hipred: Y
• hipred_score: 0.713
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.589

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ntng1

Gene ontology

• Biological process: axonogenesis;modulation of chemical synaptic transmission;synaptic membrane adhesion
• Cellular component: extracellular region;plasma membrane;anchored component of plasma membrane;Schaffer collateral - CA1 synapse;glutamatergic synapse;anchored component of presynaptic active zone membrane
• Molecular function: protein binding;cell adhesion molecule binding;cell-cell adhesion mediator activity