Mendeliome
Gene: SLC6A9 Green List (high evidence)Green List (high evidence)
26 patients from 5 families with adolescent idiopathic scoliosis. Plasma glycine concentration measured in 15 patients was elevated compared to that in 36 unaffected controls. In addition, surface electromyography in 2 affected children showed aberrant paraspinal muscle activity, which was not observed in affected adults, suggesting an etiology for the spinal curvature occurring during the developmental period.
Two different missense variants reported. Functional studies indicated a dominant negative effect. In zebrafish, mutant glyt1 protein was shown to exhibit dominant-negative effects over the wildtype protein. All slc6A9 hmz m/m fish died by 18 days postfertilization (dpf), whereas about half of the slc6A9 het m/+ fish survived to 30 dpf. Glycine levels were elevated in the slc6A9 m/m fish, and at 7 dpf the majority of the mutant fish had a lateral axial curvature. In addition, some of the slc6A9 m/+ fish also had a lateral axial curvature, which persisted through day 100 dpf. The spinal curvature was rescued by expression of wildtype SLC6A9 but not with expression of SLC6A9 with a Y206F or R662W mutation. Treatment of the slc6A9 m/m fish with benzoate, a glycine neutralizer, moderately improved the curvature phenotypeCreated: 27 Nov 2025, 11:24 a.m. | Last Modified: 27 Nov 2025, 11:24 a.m.
Panel Version: 1.3689
Glycine encephalopathy with normal serum glycine is a severe metabolic disorder characterized by arthrogryposis multiplex congenita, joint hyperlaxity, lack of neonatal respiratory effort, axial hypotonia, hypertonia with pronounced clonus, and delayed psychomotor development. Some patients may have dysmorphic facial features and/or brain imaging abnormalities. Laboratory studies show increased CSF glycine and normal or only mildly increased serum glycine.
At least 4 unrelated families and mouse model.Created: 20 Mar 2022, 12:42 p.m. | Last Modified: 20 Mar 2022, 12:42 p.m.
Panel Version: 0.11609
Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Phenotypes
Glycine encephalopathy with normal serum glycine, MIM# 617301; Scoliosis, isolated, susceptibility to, 6, MIM# 621428
Publications
Phenotypes for gene: SLC6A9 were changed from Glycine encephalopathy with normal serum glycine, MIM# 617301 to Glycine encephalopathy with normal serum glycine, MIM# 617301; Scoliosis, isolated, susceptibility to, 6, MIM# 621428
Mode of inheritance for gene: SLC6A9 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Gene: slc6a9 has been classified as Green List (High Evidence).
Phenotypes for gene: SLC6A9 were changed from to Glycine encephalopathy with normal serum glycine, MIM# 617301
Publications for gene: SLC6A9 were set to
Mode of inheritance for gene: SLC6A9 was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal
gene: SLC6A9 was added gene: SLC6A9 was added to Mendeliome_VCGS. Sources: Expert Review Green,Victorian Clinical Genetics Services Mode of inheritance for gene: SLC6A9 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.