NTNG2

netrin G2, the group of Netrins

Basic information

Region (hg38): 9:132162058-132244526

Previous symbols: [ "NTNG1" ]

Links

ENSG00000196358 ∙ NCBI:84628 ∙ OMIM:618689 ∙ HGNC:14288 ∙ Uniprot:Q96CW9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotonia (Moderate), mode of inheritance: AR
• syndromic intellectual disability (Supportive), mode of inheritance: AD
• neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotonia (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotonia	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	31372774; 31692205; 31668703

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NTNG2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NTNG2 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				11	2	13
missense		1	28	2	1	32
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding						0
Total	0	1	29	13	3

Variants in NTNG2

This is a list of pathogenic ClinVar variants found in the NTNG2 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-132166858-G-A			Likely benign (May 01, 2024)
9-132166916-G-A		Inborn genetic diseases	Uncertain significance (Apr 22, 2024)
9-132166965-G-A			Benign/Likely benign (Jul 01, 2024)
9-132166978-C-T			Likely benign (Jul 01, 2022)
9-132197958-C-G			Benign (Apr 01, 2023)
9-132197959-G-A			Likely benign (Aug 09, 2018)
9-132197994-G-A		Neurodevelopmental disorder • Neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotonia	Pathogenic/Likely pathogenic (Dec 23, 2019)
9-132198024-C-T			Uncertain significance (Mar 01, 2024)
9-132198071-T-G		Neurodevelopmental disorder • Neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotonia	Pathogenic/Likely pathogenic (Dec 23, 2019)
9-132198100-C-G			Likely benign (Jul 01, 2022)
9-132198125-C-CT		Global developmental delay;Stereotypical hand wringing;Areflexia;Generalized hypotonia • Neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotonia	Pathogenic (Dec 23, 2019)
9-132198161-G-A		Inborn genetic diseases	Uncertain significance (Sep 13, 2023)
9-132198174-T-C		Abnormality of the nervous system	Likely pathogenic (Jul 10, 2021)
9-132198198-T-C		Neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotonia • Neurodevelopmental disorder • Neurodevelopmental disorder with hypotonia, seizures, and absent language	Uncertain significance (May 29, 2020)
9-132198223-C-T			Likely benign (Aug 01, 2023)
9-132198299-C-G		Inborn genetic diseases	Uncertain significance (Mar 17, 2023)
9-132198349-C-T			Likely benign (Mar 01, 2024)
9-132198351-C-T		Neurodevelopmental disorder • Neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotonia	Likely pathogenic (Jun 01, 2022)
9-132198367-C-G			Likely benign (Apr 01, 2023)
9-132198399-G-T		Inborn genetic diseases	Uncertain significance (Dec 03, 2021)
9-132198409-C-T			Likely benign (Mar 01, 2024)
9-132198469-C-T			Benign/Likely benign (Mar 01, 2023)
9-132198470-G-A		Inborn genetic diseases	Uncertain significance (Feb 16, 2023)
9-132198490-C-T		Neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotonia	Benign (Sep 05, 2021)
9-132198494-A-C			Uncertain significance (Oct 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NTNG2	protein_coding	protein_coding	ENST00000393229	7	82588

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00134	125643	0	5	125648	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.93	191	344	0.555	0.0000233	3434
Missense in Polyphen		81	159.73	0.50711		1499
Synonymous	1.14	134	152	0.882	0.0000114	1043
Loss of Function	4.31	1	23.6	0.0423	0.00000110	252

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	0.000109	0.0000924
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000342	0.0000327
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);Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.246
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.6

Haploinsufficiency Scores

• pHI: 0.315
• hipred: Y
• hipred_score: 0.774
• ghis: 0.459

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.730

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ntng2
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hearing/vestibular/ear phenotype

Gene ontology

• Biological process: axonogenesis;modulation of chemical synaptic transmission;postsynaptic specialization assembly;synaptic membrane adhesion;regulation of presynapse assembly
• Cellular component: extracellular region;cytosol;plasma membrane;axon;intercellular bridge;anchored component of plasma membrane;Flemming body;Schaffer collateral - CA1 synapse;glutamatergic synapse;anchored component of presynaptic active zone membrane
• Molecular function: molecular_function;protein binding