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Skeletal dysplasia

Gene: CSGALNACT1

Amber List (moderate evidence)

CSGALNACT1 (chondroitin sulfate N-acetylgalactosaminyltransferase 1)
EnsemblGeneIds (GRCh38): ENSG00000147408
EnsemblGeneIds (GRCh37): ENSG00000147408
OMIM: 616615, Gene2Phenotype
CSGALNACT1 is in 3 panels

3 reviews

Michael Oldridge (NHS)

Green List (high evidence)

4 reported unrelated cases with mild skeletal dysplasia, joint laxity and advanced bone age, recessive loss of function variants identified. functional analyses show significantly reduced enzyme activity.
Created: 29 Jan 2021, 5:59 p.m. | Last Modified: 29 Jan 2021, 5:59 p.m.
Panel Version: 2.80

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Skeletal dysplasia, mild, with joint laxity and advanced bone age , MIM618870

Publications

Eleanor Williams (Genomics England Curator)

Green List (high evidence)

Comment on list classification: Promoting from grey to amber, but with recommendation for green rating following GMS review as there are now 4 cases reported of biallelic variants in this gene in patients with mild skeletal dysplasia.
Created: 13 Jan 2021, 3:26 p.m. | Last Modified: 13 Jan 2021, 3:26 p.m.
Panel Version: 2.45
Associated with Skeletal dysplasia, mild, with joint laxity and advanced bone age #618870 in OMIM

2 cases as reported by expert reviewer:
PMID: 27599773 Vodopiutz et al 2017 - infant with prenatal-onset disproportionate short stature, joint laxity, and radiographic findings typical for Desbuquois dysplasia was found to be compound-heterozygous for a large (55kb) intragenic deletion, and a p.Pro384Arg missense mutation in CSGALNACT1, each inherited from a parent.

PMID: 31325655 Meyer et al 2019 - 12 year old boy with a mild skeletal dysplasia, hypermobility of joints and axial malalignment of lower limbs and feet. He has consanguineous parents from Turkey. Exome sequencing revealed a biallelic frameshift mutation (NM_018371.4:c.372del, p.(His125Thrfs*9)) in CSGALNACT1. Csgalnact1−/− mice have reduced body length with shortened long bones.

In addition, PMID: 31705726 Mizumoto et al 2020 reports a further two unrelated cases presenting with short stature with advanced bone age, facial dysmorphism, and mild language delay. P2 (male) was found by WES to be compound‐heterozygous for a missense variant (c.1294G>T (p.Asp432Tyr)) and an intragenic deletion of 84kb that removes exon 4. P3 (female) was found by WES to be homozygous for a missense variant in CSGALNACT1 (c.791A>G (p.Asn264Ser) due to complete paternal isodisomy for chromosome 8, which harbors CSGALNACT1. The healthy father was heterozygous for this variant and the healthy mother was WT CSGALNACT1. P3 was also homozygous for a VPS13B variant causing a frameshift due to paternal isodisomy 8. Recessive variants in this gene Cohen syndrome but her clinical features do not overlap with this syndrome and the variant only impacts a short alternate isoform.
Created: 13 Jan 2021, 3:20 p.m. | Last Modified: 13 Jan 2021, 3:20 p.m.
Panel Version: 2.42

Phenotypes
Skeletal dysplasia, mild, with joint laxity and advanced bone age OMIM:618870; skeletal dysplasia, mild, with joint laxity and advanced bone age MONDO:0030029

Publications

Tracy Lester (Genetics laboratory, Oxford UK)

Desbuquois dysplasia with mild joint laxity - 2 cases reported plus a mouse model that recapitulates the phenotype: green gene for skeletal dysplasia panel
Sources: Expert Review
Created: 27 Feb 2020, 11:36 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Desbuquois dysplasia with mild joint laxity; non-proportionate short stature

Publications

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
Phenotypes
  • Desbuquois dysplasia with mild joint laxity
  • non-proportionate short stature
  • Skeletal dysplasia, mild, with joint laxity and advanced bone age OMIM:618870
  • skeletal dysplasia, mild, with joint laxity and advanced bone age MONDO:0030029
Tags
for-review
OMIM
616615
Clinvar variants
Variants in CSGALNACT1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

13 Jan 2021, Gel status: 2

Added Tag

Eleanor Williams (Genomics England Curator)

Tag for-review tag was added to gene: CSGALNACT1.

13 Jan 2021, Gel status: 2

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

Gene: csgalnact1 has been classified as Amber List (Moderate Evidence).

13 Jan 2021, Gel status: 0

Set Phenotypes

Eleanor Williams (Genomics England Curator)

Phenotypes for gene: CSGALNACT1 were changed from Desbuquois dysplasia with mild joint laxity; non-proportionate short stature to Desbuquois dysplasia with mild joint laxity; non-proportionate short stature; Skeletal dysplasia, mild, with joint laxity and advanced bone age OMIM:618870; skeletal dysplasia, mild, with joint laxity and advanced bone age MONDO:0030029

13 Jan 2021, Gel status: 0

Set publications

Eleanor Williams (Genomics England Curator)

Publications for gene: CSGALNACT1 were set to 27599773; 31325655

27 Feb 2020, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Tracy Lester (Genetics laboratory, Oxford UK)

gene: CSGALNACT1 was added gene: CSGALNACT1 was added to Skeletal dysplasia. Sources: Expert Review Mode of inheritance for gene: CSGALNACT1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: CSGALNACT1 were set to 27599773; 31325655 Phenotypes for gene: CSGALNACT1 were set to Desbuquois dysplasia with mild joint laxity; non-proportionate short stature