NTNG2

protein-coding

netrin G2, the group of Netrins

Gene summary

Predicted to enable cell-cell adhesion mediator activity. Predicted to be involved in several processes, including regulation of cell projection organization; regulation of neuron migration; and synaptic membrane adhesion. Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

NTNG1

MANE transcript

NM_032536.4

Inheritance

AD, AR

ClinVar variants

P:8U:63B:17

Top phenotype

Neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotonia

gnomAD constraint

pLI —, LoF o/e 0.04

Max pathogenic AF

—

Genomic locus

chr9:132,162,058-132,244,526

External References & Databases

Ensembl (ENSG00000196358)

Transcript & Mutation Effects

hg38 • Region Span ~82.5 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

syndromic intellectual disabilitySUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0000508

Submitter: Orphanet

neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotoniaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032878

Submitter: PanelApp Australia

neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotoniaMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0032878

Submitter: Ambry Genetics

neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotoniaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032878

Submitter: Labcorp Genetics (formerly Invitae)

neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotoniaDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0032878

Submitter: G2P

Clinical Genomic Database (CGD)

Neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotoniaAR

Manifestation: Craniofacial; Musculoskeletal; Neurologic

Intervention: General

Rationale: 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

Refs: 31372774; 31692205; 31668703

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NTNG2 variants in ClinVar

13 Conditions Cataloged

Inborn genetic diseasesTotal: 48

not providedTotal: 24

Neurodevelopmental disorder with behavioral abnormalities, absent speech, and hypotoniaTotal: 14

Neurodevelopmental disorderTotal: 7

not specifiedTotal: 6

Neurodevelopmental disorder with hypotonia, seizures, and absent languageTotal: 2

Developmental and epileptic encephalopathy, 27Total: 1

Generalized hypotoniaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_032536.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				15 clinvar		15
missense		6 clinvar	60 clinvar	2 clinvar		68
nonsense	1 clinvar					1
start loss						0
frameshift	1 clinvar		2 clinvar			3
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	2	6	63	17	0	88

Highest pathogenic variant AF is 0.000001399253

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 56 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_032536.4	RefSeq	NP_115925.2	7	MANE Select
ENST00000393229.4	Ensembl	ENSP00000376921.3	7	MANE Select
ENST00000922385.1	Ensembl	ENSP00000592444.1	7	Standard
ENST00000922385.2	Ensembl	ENSP00000592444.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

axonogenesis
modulation of chemical synaptic transmission
postsynaptic specialization assembly
synaptic membrane adhesion
regulation of presynapse assembly

Molecular Function

molecular_function
protein binding

Cellular Component

extracellular region
cytosol
plasma membrane
axon
intercellular bridge

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000393229
Coding exons: 7
Length: 82588
Individuals with no LoFs: 125643
Homozygous LoFs: 0
Heterozygous LoFs: 5
Defined: 125648
p: 0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.93	191	344	0.555	0.0000233	3434
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00011	0.000092	rare
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000034	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.121

Intolerance Scores

LoFtool: 0.246
RVIS EVS: -0.27
RVIS percentile EVS: 34.6

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.730

Gene Damage Prediction

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