Intellectual disability syndromic and non-syndromic
Gene: NRXN1 Green List (high evidence)Green List (high evidence)
NRXN1 encodes neurexin-1 which is a pre-synaptic adhesion molecule that plays important roles in synapse formation, maintenance, regulation, and function. Involved in both glutamatergic and GABAergic synapses implying a role in excitatory and inhibitory balance.
MONOALLELIC NEURODEVELOPMENTAL DISORDER WITH REDUCED PENETRANCE
A monoallelic disease association has been reported in a number of publications with deletions linked to neurodevelopmental and behavioural phenotypes including intellectual disability, epilepsy, autism, schizophrenia, Tourette's syndrome.
Many affected individuals inherited deletions from presumably unaffected parents, with deletions in the gene also observed in population databases.
This gene disease association has been reported as definitive by Clingen in 2019.
Reduced penetrance has been noted in publications with some quoting 10% penetrance for intellectual disability, others an odds ratio of 7.47.
There are 3 main isoforms in humans - alpha, beta and gamma. Alpha is the longest isoform and 5 prime deletions of NRXN1 correspond to loss of alpha transcript. These deletions have been most extensively described in affected individuals. Supportive functional studies include mouse models, iHuman induced pluripotent stem (hiPS) -derived neurons from affected individuals and zebrafish studies.
Functional studies supporting a deleterious nature of deletions of other isoforms have been published although the mechanism of disease is less clear.Created: 25 Jun 2026, 2:05 p.m. | Last Modified: 25 Jun 2026, 2:05 p.m.
Panel Version: 2.104
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Phenotypes
Neurodevelopmental disorder, MONDO:0700092, NRXN1-related
Publications
Green List (high evidence)
19896112 - report one individual with compound het variants and Pitt-Hopkins-like syndromic ID (no seizures)
21964664 - report 2 affected siblings with compound het variants and severe early onset epilepsy, profound developmental delay, gastroesophageal reflux disease, constipation, and early onset puberty.
35101781 - report 2 siblings with homozygous exonic deletions. One with infantile spasms and neurodevelopmental disorder. Other with autism spectrum disorder.
22337556 - report one individual with autism, ID and epilepsy and compound het variants
25486015 - report one individual with homozygous exonic deletion and ID/dysmorphic featuresCreated: 28 Mar 2022, 11:07 a.m.
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Phenotypes
Pitt-Hopkins-like syndrome 2 - MIM#614325
Publications
Source Genetic Health Queensland was removed from NRXN1. Source Literature was added to NRXN1. Mode of inheritance for gene NRXN1 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Phenotypes for gene: NRXN1 were changed from Pitt-Hopkins-like syndrome 2 - MIM#614325 to Pitt-Hopkins-like syndrome 2 - MIM#614325; Complex neurodevelopmental disorder, MONDO:0100038, NRXN1-related
Gene: nrxn1 has been classified as Green List (High Evidence).
Phenotypes for gene: NRXN1 were changed from to Pitt-Hopkins-like syndrome 2 - MIM#614325
Publications for gene: NRXN1 were set to
Mode of inheritance for gene: NRXN1 was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal
gene: NRXN1 was added gene: NRXN1 was added to Intellectual disability, syndromic and non-syndromic_GHQ. Sources: Expert Review Green,Genetic Health Queensland Mode of inheritance for gene: NRXN1 was set to Unknown
If promoting or demoting a gene, please provide comments to justify a decision to move it.
Genes included in a Genomics England gene panel for a rare disease category (green list) should fit the criteria A-E outlined below.
These guidelines were developed as a combination of the ClinGen DEFINITIVE evidence for a causal role of the gene in the disease(a), and the Developmental Disorder Genotype-Phenotype (DDG2P) CONFIRMED DD Gene evidence level(b) (please see the original references provided below for full details). These help provide a guideline for expert reviewers when assessing whether a gene should be on the green or the red list of a panel.
A. There are plausible disease-causing mutations(i) within, affecting or encompassing an interpretable functional region(ii) of this gene identified in multiple (>3) unrelated cases/families with the phenotype(iii).
OR
B. There are plausible disease-causing mutations(i) within, affecting or encompassing cis-regulatory elements convincingly affecting the expression of a single gene identified in multiple (>3) unrelated cases/families with the phenotype(iii).
OR
C. As definitions A or B but in 2 or 3 unrelated cases/families with the phenotype, with the addition of convincing bioinformatic or functional evidence of causation e.g. known inborn error of metabolism with mutation in orthologous gene which is known to have the relevant deficient enzymatic activity in other species; existence of an animal model which recapitulates the human phenotype.
AND
D. Evidence indicates that disease-causing mutations follow a Mendelian pattern of causation appropriate for reporting in a diagnostic setting(iv).
AND
E. No convincing evidence exists or has emerged that contradicts the role of the gene in the specified phenotype.
(i)Plausible disease-causing mutations: Recurrent de novo mutations convincingly affecting gene function. Rare, fully-penetrant mutations - relevant genotype never, or very rarely, seen in controls. (ii) Interpretable functional region: ORF in protein coding genes miRNA stem or loop. (iii) Phenotype: the rare disease category, as described in the eligibility statement. (iv) Intermediate penetrance genes should not be included.
It’s assumed that loss-of-function variants in this gene can cause the disease/phenotype unless an exception to this rule is known. We would like to collect information regarding exceptions. An example exception is the PCSK9 gene, where loss-of-function variants are not relevant for a hypercholesterolemia phenotype as they are associated with increased LDL-cholesterol uptake via LDLR (PMID: 25911073).
If a curated set of known-pathogenic variants is available for this gene-phenotype, please contact us at panelapp@genomicsengland.co.uk
We classify loss-of-function variants as those with the following Sequence Ontology (SO) terms:
Term descriptions can be found on the PanelApp homepage and Ensembl.
If you are submitting this evaluation on behalf of a clinical laboratory please indicate whether you report variants in this gene as part of your current diagnostic practice by checking the box
Standardised terms were used to represent the gene-disease mode of inheritance, and were mapped to commonly used terms from the different sources. Below each of the terms is described, along with the equivalent commonly-used terms.
A variant on one allele of this gene can cause the disease, and imprinting has not been implicated.
A variant on the paternally-inherited allele of this gene can cause the disease, if the alternate allele is imprinted (function muted).
A variant on the maternally-inherited allele of this gene can cause the disease, if the alternate allele is imprinted (function muted).
A variant on one allele of this gene can cause the disease. This is the default used for autosomal dominant mode of inheritance where no knowledge of the imprinting status of the gene required to cause the disease is known. Mapped to the following commonly used terms from different sources: autosomal dominant, dominant, AD, DOMINANT.
A variant on both alleles of this gene is required to cause the disease. Mapped to the following commonly used terms from different sources: autosomal recessive, recessive, AR, RECESSIVE.
The disease can be caused by a variant on one or both alleles of this gene. Mapped to the following commonly used terms from different sources: autosomal recessive or autosomal dominant, recessive or dominant, AR/AD, AD/AR, DOMINANT/RECESSIVE, RECESSIVE/DOMINANT.
A variant on one allele of this gene can cause the disease, however a variant on both alleles of this gene can result in a more severe form of the disease/phenotype.
A variant in this gene can cause the disease in males as they have one X-chromosome allele, whereas a variant on both X-chromosome alleles is required to cause the disease in females. Mapped to the following commonly used term from different sources: X-linked recessive.
A variant in this gene can cause the disease in males as they have one X-chromosome allele. A variant on one allele of this gene may also cause the disease in females, though the disease/phenotype may be less severe and may have a later-onset than is seen in males. X-linked inactivation and mosaicism in different tissues complicate whether a female presents with the disease, and can change over their lifetime. This term is the default setting used for X-linked genes, where it is not known definitately whether females require a variant on each allele of this gene in order to be affected. Mapped to the following commonly used terms from different sources: X-linked dominant, x-linked, X-LINKED, X-linked.
The gene is in the mitochondrial genome and variants within this can cause this disease, maternally inherited. Mapped to the following commonly used term from different sources: Mitochondrial.
Mapped to the following commonly used terms from different sources: Unknown, NA, information not provided.
For example, if the mode of inheritance is digenic, please indicate this in the comments and which other gene is involved.