Groopman et al 2019 - Genes with diagnostic variants (Version 0.8)

Description

REFERENCE ONLY PANEL

Gene list from Groopman et al 2019 (PMID: 30586318)
Table S7 Diagnostic genetic findings and clinical implications

In this study they performed exome sequencing in a combined cohort of more than 3000 patients with chronic kidney disease.

Genes containing a diagnostic variant listed in Table S7 have been included on this panel. The ratings are as follows:
Green - 3 or more cases reported in Table S7
Amber - 2 cases reported in Table S7
Red - 1 case reported in Table S7

Note: the cases may have presented with different clinical phenotypes

Panel Activity

1 reviewer

Eleanor Williams (Genomics England Curator)

Group: Other
Workplace: Other

66 Entities

66 reviewed, 21 green

List	Entity	Reviews	Mode of inheritance	Details
Filter Entities 66 Entitiess
Green Green List (high evidence)	CLCN5	1 review	X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)	Sources Expert review green Expert Review Green Literature Phenotypes Tubulointerstitial disease Dent disease Nephropathy of unknown origin Glomerulopathy MIM 300009 Tags
Green Green List (high evidence)	COL4A3	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review green Expert Review Green Literature Phenotypes Hypertensive nephropathy MIM 104200, 203780 Congenital or cystic renal disease Nephropathy of unknown origin Glomerulopathy Thin basement membrane disease Alport syndrome, autosomal dominant/recessive 141200 Tags
Green Green List (high evidence)	COL4A4	1 review	BOTH monoallelic and biallelic, autosomal or pseudoautosomal	Sources Expert review green Expert Review Green Literature Phenotypes MIM 203780 Hypertensive nephropathy Congenital or cystic renal disease Nephropathy of unknown origin Glomerulopathy Thin basement membrane disease Alport syndrome, autosomal dominant/recessive 141200 Tags
Green Green List (high evidence)	COL4A5	1 review	X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)	Sources Expert review green Expert Review Green Literature Phenotypes MIM 301050 Congenital or cystic renal disease Nephropathy of unknown origin Alport syndrome, X-linked Glomerulopathy Tags
Green Green List (high evidence)	CREBBP	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review green Expert Review Green Literature Phenotypes Congenital or cystic renal disease Rubinstein-Taybi syndrome 1 Nephropathy of unknown origin MIM 180849 Glomerulopathy Tags
Green Green List (high evidence)	DHCR7	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Expert review green Expert Review Green Literature Phenotypes Tubulointerstitial disease Congenital or cystic renal disease Nephropathy of unknown origin MIM 270400 Smith-Lemli-Opitz syndrome Tags
Green Green List (high evidence)	EYA1	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review green Expert Review Green Literature Phenotypes Congenital or cystic renal disease MIM 113650 Branchiootorenal syndrome 1 with or without cataracts Tags
Green Green List (high evidence)	GLA	1 review	X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)	Sources Expert review green Expert Review Green Literature Phenotypes Tubulointerstitial disease Other Fabry disease MIM 301500 Tags
Green Green List (high evidence)	HBB	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Expert review green Expert Review Green Literature Phenotypes Other Nephropathy of unknown origin Sickle cell disease MIM 603903 Tags
Green Green List (high evidence)	HNF1A	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review green Expert Review Green Literature Phenotypes MODY type III Nephropathy of unknown origin Diabetic nephropathy MIM 600496 Tags
Green Green List (high evidence)	INF2	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review green Expert Review Green Literature Phenotypes Glomerulosclerosis focal segmental 5 Nephropathy of unknown origin Hypertensive nephropathy Glomerulopathy MIM 613237 Tags
Green Green List (high evidence)	NPHP3	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Expert review green Expert Review Green Literature Phenotypes MIM 604387 Nephronophthisis 3 Nephropathy of unknown origin Glomerulopathy Tags
Green Green List (high evidence)	NPHP4	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Expert review green Expert Review Green Literature Phenotypes Nephropathy of unknown origin MIM 606966 Nephronophthisis 4 Tags
Green Green List (high evidence)	NPHS2	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Expert review green Expert Review Green Literature Phenotypes Nephropathy of unknown origin Hypertensive nephropathy Glomerulopathy Nephrotic syndrome type 2 MIM 600995 Tags
Green Green List (high evidence)	PAX2	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review green Expert Review Green Literature Phenotypes MIM 616002 Congenital or cystic renal disease Nephropathy of unknown origin Glomerulosclerosis focal segmental 7 Glomerulopathy Papillorenal syndrome 120330 Tags
Green Green List (high evidence)	PKD1	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review green Expert Review Green Literature Phenotypes Congenital or cystic renal disease Nephropathy of unknown origin Polycystic kidney disease 1 MIM 173900 Tags
Green Green List (high evidence)	PKD2	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review green Expert Review Green Literature Phenotypes Polycystic kidney disease 2 Congenital or cystic renal disease MIM 613095 Tags
Green Green List (high evidence)	PKHD1	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Expert review green Expert Review Green Literature Phenotypes Polycystic kidney disease, autosomal recessive Congenital or cystic renal disease Nephropathy of unknown origin MIM 263200 Tags
Green Green List (high evidence)	SLC12A3	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Expert review green Expert Review Green Literature Phenotypes Tubulointerstitial disease MIM 263800 Glomerulopathy Gitelman syndrome Tags
Green Green List (high evidence)	TRPC6	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review green Expert Review Green Literature Phenotypes MIM 603965 Nephropathy of unknown origin Glomerulopathy Glomerulosclerosis focal segmental 2 Tags
Green Green List (high evidence)	UMOD	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review green Expert Review Green Literature Phenotypes Tubulointerstitial disease Hypertensive nephropathy 162000 Congenital or cystic renal disease 603860 Nephropathy of unknown origin Autosomal dominant tubulointerstitial kidney disease, UMOD-associated Glomerulopathy MIM 609886 Tags
Amber Amber List (moderate evidence)	AVP	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Exper review amber Expert Review Amber Literature Phenotypes MIM 125700 Congenital or cystic renal disease Nephropathy of unknown origin Diabetes insipidus, neurohypophyseal Tags
Amber Amber List (moderate evidence)	CRB2	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Exper review amber Expert Review Amber Literature Phenotypes Focal segmental glomerulosclerosis 9 Glomerulopathy MIM 616220 Tags
Amber Amber List (moderate evidence)	NF1	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Exper review amber Expert Review Amber Literature Phenotypes Congenital or cystic renal disease MIM 162200 Neurofibromatosis type 1 Tags
Amber Amber List (moderate evidence)	NPHS1	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Exper review amber Expert Review Amber Literature Phenotypes MIM 256300 Nephrotic syndrome type 1 Glomerulopathy Tags
Amber Amber List (moderate evidence)	PTPN11	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Exper review amber Expert Review Amber Literature Phenotypes Noonan syndrome 1 MIM 163950 Nephropathy of unknown origin Diabetic nephropathy Tags
Amber Amber List (moderate evidence)	SLC3A1	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Exper review amber Expert Review Amber Literature Phenotypes Tubulointerstitial disease Congenital or cystic renal disease Hypertensive nephropathy Cystinuria MIM 220100 Tags
Red Red List (low evidence)	ACTG2	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes MIM 155310 Congenital or cystic renal disease Visceral myopathy Tags
Red Red List (low evidence)	ANOS1	1 review	X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)	Sources Expert review red Expert Review Red Literature Phenotypes MIM 308700 Glomerulopathy Hypogonadotropic hypogonadism 1 with or without anosmia (Kallmann syndrome 1) Tags
Red Red List (low evidence)	APOA1	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes MIM 105200 Amyloidosis, renal Glomerulopathy Tags
Red Red List (low evidence)	ATP6V1B1	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Expert review red Expert Review Red Literature Phenotypes Tubulointerstitial disease MIM 267300 Renal tubular acidosis with deafness Tags
Red Red List (low evidence)	CDKN1C	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Beckwith-Wiedemann syndrome MIM 130650 Glomerulopathy Tags
Red Red List (low evidence)	COL11A1	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Stickler syndrome type II Congenital or cystic renal disease MIM 604841 Tags
Red Red List (low evidence)	FANCB	1 review	X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)	Sources Expert review red Expert Review Red Literature Phenotypes Congenital or cystic renal disease Fanconi anemia complementation group B MIM 300514 Tags
Red Red List (low evidence)	FGFR2	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Nephropathy of unknown origin MIM 101600 Pfeiffer syndrome Tags
Red Red List (low evidence)	HNF1B	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Congenital or cystic renal disease MIM 137920 Renal cysts and diabetes syndrome Tags
Red Red List (low evidence)	HNF4A	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes MODY type I Nephropathy of unknown origin MIM 125850 Tags
Red Red List (low evidence)	IQCB1	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Expert review red Expert Review Red Literature Phenotypes Congenital or cystic renal disease MIM 609254 Senior-Loken syndrome 5 Tags
Red Red List (low evidence)	JAG1	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Congenital or cystic renal disease Alagille syndrome 1 MIM 118450 Tags
Red Red List (low evidence)	KANSL1	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Koolen-De Vries syndrome Congenital or cystic renal disease MIM 610443 Tags
Red Red List (low evidence)	KLHL3	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Other MIM 614495 Pseudohypoaldosteronism type IID Tags
Red Red List (low evidence)	KRAS	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes MIM 609942 Glomerulopathy Noonan syndrome 3 Tags
Red Red List (low evidence)	LMX1B	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Nail-patella syndrome MIM 161200 Glomerulopathy Tags
Red Red List (low evidence)	LRIG2	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Expert review red Expert Review Red Literature Phenotypes Congenital or cystic renal disease MIM 615112 Urofacial syndrome 2 Tags
Red Red List (low evidence)	MC4R	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Obesity autosomal dominant Nephropathy of unknown origin MIM 601665 Tags
Red Red List (low evidence)	MKKS	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Expert review red Expert Review Red Literature Phenotypes MIM 605231 Nephropathy of unknown origin Bardet-Biedl syndrome 6 Tags
Red Red List (low evidence)	MYCN	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes MIM 164280 Diabetic nephropathy Feingold syndrome 1 Tags
Red Red List (low evidence)	MYH9	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Fechtner syndrome Epstein syndrome Nephropathy of unknown origin 153640 MIM 153650 Tags
Red Red List (low evidence)	OCRL	1 review	X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)	Sources Expert review red Expert Review Red Literature Phenotypes Nephropathy of unknown origin MIM 300555 Dent disease 2 Tags
Red Red List (low evidence)	PLCE1	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Expert review red Expert Review Red Literature Phenotypes MIM 610725 Glomerulopathy Nephrotic syndrome type 3 Tags
Red Red List (low evidence)	REN	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Tubulointerstitial disease MIM 613092 Autosomal dominant tubulointerstitial kidney disease, REN-associated Tags
Red Red List (low evidence)	RERE	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Congenital or cystic renal disease MIM 616975 Neurodevelopmental disorder with or without anomalies of the brain, eye, or heart Tags
Red Red List (low evidence)	ROBO2	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Congenital or cystic renal disease Vesicoureteral reflux 2 MIM 610878 Tags
Red Red List (low evidence)	SALL1	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Townes-Brocks syndrome 1 Glomerulopathy MIM 107480 Tags
Red Red List (low evidence)	SEC61A1	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Congenital or cystic renal disease MIM 617056 Hyperuricemic nephropathy familial juvenile 4 Tags
Red Red List (low evidence)	SLC16A12	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Tubulointerstitial disease MIM 612018 Cataract 47 juvenile with microcornea Tags
Red Red List (low evidence)	SLC26A1	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Expert review red Expert Review Red Literature Phenotypes MIM 167030 Nephropathy of unknown origin Nephrolithiasis calcium oxalate Tags
Red Red List (low evidence)	SLC34A3	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Expert review red Expert Review Red Literature Phenotypes MIM 241530 Nephropathy of unknown origin Hypophosphatemic rickets with hypercalciuria Tags
Red Red List (low evidence)	SLC4A1	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Tubulointerstitial disease Renal tubular acidosis distal, autosomal dominant MIM 179800 Tags
Red Red List (low evidence)	SLC7A9	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Tubulointerstitial disease Cystinuria MIM 220100 Tags
Red Red List (low evidence)	SMARCAL1	1 review	BOTH monoallelic and biallelic, autosomal or pseudoautosomal	Sources Expert review red Expert Review Red Literature Phenotypes MIM 242900 Schimke immunoosseous dysplasia Glomerulopathy Tags
Red Red List (low evidence)	SMC1A	1 review	X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)	Sources Expert review red Expert Review Red Literature Phenotypes Congenital or cystic renal disease MIM 300590 Cornelia de Lange syndrome 2 Tags
Red Red List (low evidence)	TSC2	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes Other MIM 613254 Tuberous sclerosis 2 Tags
Red Red List (low evidence)	TTC21B	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Expert review red Expert Review Red Literature Phenotypes Nephropathy of unknown origin Nephronophthisis 12 MIM 613820 Tags
Red Red List (low evidence)	WDR19	1 review	BIALLELIC, autosomal or pseudoautosomal	Sources Expert review red Expert Review Red Literature Phenotypes Congenital or cystic renal disease MIM 614377 Nephronophthisis 13 Tags
Red Red List (low evidence)	WT1	1 review	MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown	Sources Expert review red Expert Review Red Literature Phenotypes MIM 256370 Nephrotic syndrome type 4 Glomerulopathy Tags

Groopman et al 2019 - Genes with diagnostic variants (Version 0.8)

1 reviewer

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66 reviewed, 21 green

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