Mendeliome
Gene: COL9A3 Green List (high evidence)Green List (high evidence)
New genotype-phenotype correlation reported in PMID: 33633367 - Heterozygous COL9A3 variants cause severe peripheral vitreoretinal degeneration and retinal detachment:
c.1107+1G>C and Gly130Ser
cDNA studies of the splice variant demonstrated an in-frame deletion in the COL2 domain, and the missense variant occurred in the COL3 domain.
In Family 1, 14 affected individuals of Filipino/Australian ethnicity presented with vitreoretinal degeneration in a pattern suggestive of autosomal dominant inheritance (Fig. 1A). Affected individuals had extensive bilateral lattice vitreoretinal degeneration, with an abnormal vitreoretinal interface particularly at the vitreous base, where the retina was thinned and prone to tears. In Family 2 from New Zealand, three affected members of European background presented with vitreoretinal degeneration and retinal detachment, also in a pattern suggestive of autosomal dominant inheritance (Fig. 1B). In affected individuals in both families with extensive vitreoretinal degeneration, laser intervention or cryotherapy was recommended to prevent further vitreoretinal detachment or tearing.Created: 7 Jun 2021, 5:35 a.m. | Last Modified: 7 Jun 2021, 5:35 a.m.
Panel Version: 0.7891
Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Phenotypes
Epiphyseal dysplasia, multiple, 3, with or without myopathy, AD, MIM# 600969; Stickler syndrome, AR; Deafness, AD; Peripheral vitreoretinal degeneration and retinal detachment, AD
Publications
Green List (high evidence)
Mono-allelic variants are associated with MED. Association with isolated deafness not established.
Bi-allelic variants are associated with Stickler syndrome and possibly isolated deafness, though difficult to be certain.Created: 4 Mar 2021, 5:39 a.m. | Last Modified: 4 Mar 2021, 5:39 a.m.
Panel Version: 0.6541
Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Phenotypes
Epiphyseal dysplasia, multiple, 3, with or without myopathy, MIM# 600969; Stickler syndrome, type VI, MIM# 620022; Deafness
Publications
Green List (high evidence)
Further hearing loss cases:
PMID: 33078831 - Wonkam et al 2020 - report 2 unrelated patients from Cameroon with autosomal recessive non-syndromic hearing impairment and a homozygous c.G406A, p.G136S variant in COL9A3. This variant is rare (ExAC_AFR MAF = 0, ExAC_ASI MAF = 0.001, Cameroonian controls MAF (N = 129) = 0). However, the authors report that further investigation of these patients is needed to exclude Stickler syndrome.
Older publication which may have been missed:
PMID: 15917166 - Asamura et al 2005 - direct-sequencing of COL9A3 gene in 159 non-syndromic sensorineural deafness patients (Japanese and Korean) and 150 normal controls. 2 possible disease-causing mutations were identified in patients with moderate progressive bilateral sensorineural hearing impairment in all frequencies: a homozygous in-frame deletion of three amino acid residues (G181-P183 del) in one patient (with consanguineous parents) and a heterozygous missense mutation (D617E) found in 2 independent autosomal dominant families. No segregation data.Created: 3 Mar 2021, 12:28 p.m. | Last Modified: 3 Mar 2021, 12:28 p.m.
Panel Version: 0.6539
Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal
Phenotypes
autosomal recessive non-syndromic hearing impairment
Publications
Phenotypes for gene: COL9A3 were changed from Epiphyseal dysplasia, multiple, 3, with or without myopathy, MIM# 600969; Stickler syndrome AR; Deafness AD; Peripheral vitreoretinal degeneration and retinal detachment, AD to Epiphyseal dysplasia, multiple, 3, with or without myopathy, MIM# 600969; Stickler syndrome, type VI, MIM# 620022; Deafness AD; Peripheral vitreoretinal degeneration and retinal detachment, AD
Phenotypes for gene: COL9A3 were changed from Epiphyseal dysplasia, multiple, 3, with or without myopathy, MIM# 600969; Stickler syndrome; Deafness to Epiphyseal dysplasia, multiple, 3, with or without myopathy, MIM# 600969; Stickler syndrome AR; Deafness AD; Peripheral vitreoretinal degeneration and retinal detachment, AD
Publications for gene: COL9A3 were set to 30450842; 31090205; 24273071; 10090888; 15551337; 33078831; 15917166
Gene: col9a3 has been classified as Green List (High Evidence).
Phenotypes for gene: COL9A3 were changed from to Epiphyseal dysplasia, multiple, 3, with or without myopathy, MIM# 600969; Stickler syndrome; Deafness
Publications for gene: COL9A3 were set to
Mode of inheritance for gene: COL9A3 was changed from Unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
gene: COL9A3 was added gene: COL9A3 was added to Mendeliome_VCGS. Sources: Expert Review Green,Victorian Clinical Genetics Services Mode of inheritance for gene: COL9A3 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.