Congenital anomalies of the kidney and urinary tract (CAKUT) Nonsyndromic

Gene: CHD1L

Red List (low evidence)

CHD1L (chromodomain helicase DNA binding protein 1 like)
EnsemblGeneIds (GRCh38): ENSG00000131778
EnsemblGeneIds (GRCh37): ENSG00000131778
OMIM: 613039, Gene2Phenotype
CHD1L is in 2 panels

3 reviews

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Comment when marking as ready: The population variant frequencies are out of keeping for a Mendelian disorder.
Created: 18 Jun 2020, 10:36 a.m. | Last Modified: 18 Jun 2020, 10:36 a.m.
Panel Version: 0.72

Melanie Marty (Victorian Clinical Genetics Services)

I don't know

Review of this gene during variant curation. The 6 missense variants reported in the two papers (PMID: 22146311, 24429398) are very common in gnomAD:
CHD1L:c.2098G>A; p.Gly700Arg - 1110 hets, 5 hom
CHD1L:c.2295A>G; p.Ile765Met - 468 hets, 1 hom
CHD1L:c.2479A>G; p.Ile827Val – 725 hets, 2 hom
CHD1L:c.998C>G; p.Pro333Arg – 1 het, 0 hom
CHD1L:c.1199A>G; p.Glu400Gly – 3 hets, 0 hom
CHD1L:c.1551A>G; p.Ile517Met – 195 hets, 0 hom
I could not find any other papers for this gene in association with CAKUT. ClinVar only has 1 frameshift variant reported as pathogenic from research in 2001 for an unrelated condition (short stature), the other variants reported in this gene are VUS or LB/B.
Created: 18 Jun 2020, 3:48 a.m. | Last Modified: 18 Jun 2020, 3:48 a.m.
Panel Version: 0.71

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
CAKUT

Publications

Chirag Patel (Genetic Health Queensland)

Green List (high evidence)

Two of three novel heterozygous missense variants identified in 3 CAKUT patients. Quantitative messenger RNA analysis demonstrated high CHD1L expression in human fetal kidneys, and levels were four times higher than in adult kidneys. In the human embryo at 7-11 weeks gestation, CHD1L immunolocalized in the early ureteric bud and the S- and comma-shaped bodies, critical stages of kidney development. In normal postnatal sections, CHD1L was expressed in the cytoplasm of tubular cells in all tubule segments. CHD1L expression appeared higher in the hydronephrotic kidney of one patient with a hypofunctional CHD1L variant than in normal kidneys, recapitulating high fetal levels.

5 unrelated patients with CAKUT and CHD1L
Created: 16 Jan 2020, 3:31 a.m. | Last Modified: 16 Jan 2020, 3:31 a.m.
Panel Version: 0.27

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
CAKUT

Publications

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Red
  • Victorian Clinical Genetics Services
Phenotypes
  • CAKUT
Tags
disputed
OMIM
613039
Clinvar variants
Variants in CHD1L
Penetrance
None
Publications
Panels with this gene

History Filter Activity

18 Jun 2020, Gel status: 1

Entity classified by Genomics England curator

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Gene: chd1l has been classified as Red List (Low Evidence).

18 Jun 2020, Gel status: 1

Entity classified by Genomics England curator

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Gene: chd1l has been classified as Red List (Low Evidence).

18 Jun 2020, Gel status: 3

Added Tag

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Tag disputed tag was added to gene: CHD1L.

16 Jan 2020, Gel status: 3

Set Phenotypes

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Phenotypes for gene: CHD1L were changed from CAKUT to CAKUT

16 Jan 2020, Gel status: 3

Entity classified by Genomics England curator

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Gene: chd1l has been classified as Green List (High Evidence).

16 Jan 2020, Gel status: 3

Set Phenotypes

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Phenotypes for gene: CHD1L were changed from to CAKUT

16 Jan 2020, Gel status: 3

Set publications

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Publications for gene: CHD1L were set to

16 Jan 2020, Gel status: 3

Set mode of inheritance

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

Mode of inheritance for gene: CHD1L was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

17 Nov 2019, Gel status: 3

Created, Added New Source, Set mode of inheritance

Zornitza Stark (Victorian Clinical Genetics Services; Australian Genomics)

gene: CHD1L was added gene: CHD1L was added to Congenital anomalies of the kidney and urinary tract (CAKUT) Nonsyndromic_VCGS. Sources: Expert Review Green,Victorian Clinical Genetics Services Mode of inheritance for gene: CHD1L was set to Unknown