Description
This gene panel is in development and will also cover biliary atresia and neonatal liver dysfunction. As a reviewer, please add new genes related to this disease or contact panelapp@genomicsengland.co.uk if you would like to submit a gene list for this panel.

Neonatal cholestasis eligibility inclusion criteria (from rare disease eligibility criteria v1.8.1)
- Neonatal cholestasis in which a known genetic disease has been excluded and in which a monogenic cause is considered likely by a specialist Liver Unit. 

Neonatal cholestasis eligibility exclusion criteria 
- Infective causes after excluding known genetic disease. 

Prior genetic testing guidance - Results should have been reviewed for all genetic tests undertaken, including disease-relevant genes in exome sequencing data. The patient is not eligible if they have a molecular diagnosis for their condition. 

- Genetic testing should continue according to routine local practice for this phenotype regardless of recruitment to the project; results of these tests must be submitted via the ‘Genetic investigations’ section of the data capture tool to allow comparison of WGS with current standard testing. 

PLEASE NOTE: The sensitivity of WGS compared to current diagnostic genetic testing has not yet been established. It is therefore important that tests which are clinically indicated under local standard practice continue to be carried out. Neonatal cholestasis eligibility prior genetic testing genes 

Closing statement These requirements will be kept under continual review during the main programme and may be subject to change.

5 reviewers

  • Ellen McDonagh (Genomics England Curator)

    Group: other
    Workplace: other

  • Thalia Antoniadi (West Midlands Regional Genetics Laboratory)

    Group: NHS Genomic Medicine Centre
    Workplace: NHS diagnostic lab

  • Ellen Thomas (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Rachel Jones (GSTT)

    Group: NHS Genomic Medicine Centre
    Workplace: NHS clinical service

  • Jane Hartley (Birmingham Women and Children's Hospital)

    Group: Other NHS organisation
    Workplace: NHS clinical service

86 genes

58 reviewed, 10 green

List Gene Reviews Mode of inheritance Details
86 genes
Green Green List (high evidence)
ABCB11
2 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Illumina TruGenome Clinical Sequencing Services
  • Victorian Clinical Genetics Services
  • UKGTN
  • Emory Genetics Laboratory
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Neonatal and Adult Cholestasis
  • Cholestasis, benign recurrent intrahepatic, 2, 605479
  • Cholestasis, progressive familial intrahepatic 2, 601847
  • Cholestasis, Progressive Familial Intrahepatic 2
  • Familial Intrahepatic Cholestasis
Green Green List (high evidence)
ABCB4
2 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Illumina TruGenome Clinical Sequencing Services
  • Victorian Clinical Genetics Services
  • UKGTN
  • Radboud University Medical Center, Nijmegen
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
  • Cholestasis, intrahepatic, of pregnancy, 3, 614972
  • Cholestasis, progressive familial intrahepatic 3, 602347
  • Cholestasis, Progressive Familial Intrahepatic 3
  • Familial Intrahepatic Cholestasis
  • Progressive Familial Intrahepatic Cholestasis
Green Green List (high evidence)
ATP8B1
2 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Illumina TruGenome Clinical Sequencing Services
  • UKGTN
  • Radboud University Medical Center, Nijmegen
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
  • Cholestasis, benign recurrent intrahepatic, 243300
  • Cholestasis, intrahepatic, of pregnancy, 1, 147480
  • Cholestasis, progressive familial intrahepatic 1, 211600
  • Cholestasis, Progressive Familial Intrahepatic 1
  • Familial Intrahepatic Cholestasis
Green Green List (high evidence)
HNF1B
4 reviews
2 green 1 red
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Green
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Renal cysts and diabetes syndrome 137920
Green Green List (high evidence)
VPS33B
2 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Illumina TruGenome Clinical Sequencing Services
  • UKGTN
  • Emory Genetics Laboratory
  • Radboud University Medical Center, Nijmegen
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
  • Arthrogryposis, renal dysfunction, and cholestasis 1, 208085
  • Arthrogryposis, Renal Dysfunction, and Cholestasis 1
  • Arthrogryposis, Renal Dysfunction, And Cholestasis 1
  • Arthrogryposis, Renal Dysfunction, and Cholestasis Syndrome
Green Green List (high evidence)
AKR1D1
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • UKGTN
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
  • Expert Review Green
Phenotypes
  • Neonatal and Adult Cholestasis
  • Bile acid synthesis defect, congenital, 2
  • Bile acid synthesis defect, congenital, 2 235555
Green Green List (high evidence)
ALDOB
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
  • Expert Review Green
  • UKGTN
Phenotypes
  • Neonatal and Adult Cholestasis
  • Fructose intolerance, hereditary
Green Green List (high evidence)
NR1H4
2 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • UKGTN
  • Radboud University Medical Center, Nijmegen
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
  • Cholestasis, progressive familial intrahepatic 5, 617049
  • Cholestasis, Progressive Familial Intrahepatic 5
Green Green List (high evidence)
TJP2
2 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Radboud University Medical Center, Nijmegen
  • UKGTN
  • Victorian Clinical Genetics Services
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
  • Cholestasis, progressive familial intrahepatic 4, 615878
  • Cholestasis, Progressive Familial Intrahepatic 4
Green Green List (high evidence)
VIPAS39
2 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • UKGTN
  • Victorian Clinical Genetics Services
  • Emory Genetics Laboratory
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Neonatal and Adult Cholestasis
  • Arthrogryposis, renal dysfunction, and cholestasis 2, 613404
  • Arthrogryposis, Renal Dysfunction, and Cholestasis 2
Amber Amber List (moderate evidence)
BAAT
1 review
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Victorian Clinical Genetics Services
  • Emory Genetics Laboratory
  • UKGTN
Phenotypes
  • Neonatal and Adult Cholestasis
  • Hypercholanemia, Familial
Amber Amber List (moderate evidence)
CLDN1
1 review
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
  • UKGTN
Phenotypes
  • Neonatal and Adult Cholestasis
  • Ichthyosis, leukocyte vacuoles, alopecia and sclerosing cholangitis
Amber Amber List (moderate evidence)
CYP27A1
1 review
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Victorian Clinical Genetics Services
  • Emory Genetics Laboratory
  • UKGTN
Phenotypes
  • Neonatal and Adult Cholestasis
  • Cerebrotendinous xanthomatosis
Amber Amber List (moderate evidence)
CYP7B1
1 review
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Victorian Clinical Genetics Services
  • UKGTN
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
  • Bile acid synthesis defect, congenital, 3
Amber Amber List (moderate evidence)
HSD3B7
1 review
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • UKGTN
  • Victorian Clinical Genetics Services
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
  • Bile acid sythesis defect, congenital, 1
Amber Amber List (moderate evidence)
JAG1
3 reviews
3 green
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Victorian Clinical Genetics Services
  • Other
  • Emory Genetics Laboratory
  • UKGTN
Phenotypes
  • Alagille syndrome
  • Neonatal and Adult Cholestasis
  • Alagille syndrome 1
Amber Amber List (moderate evidence)
NOTCH2
2 reviews
2 green
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
  • UKGTN
Phenotypes
  • Neonatal and Adult Cholestasis
  • Alagille syndrome 2
Amber Amber List (moderate evidence)
NPC1
2 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • UKGTN
  • Victorian Clinical Genetics Services
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
  • Niemann-Pick disease type C1
Amber Amber List (moderate evidence)
NPC2
2 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Victorian Clinical Genetics Services
  • Emory Genetics Laboratory
  • UKGTN
Phenotypes
  • Neonatal and Adult Cholestasis
  • Niemann-Pick disease type C2
Amber Amber List (moderate evidence)
PEX1
1 review
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
  • UKGTN
Phenotypes
  • Neonatal and Adult Cholestasis
  • Peroxisome Biogenesis Disorder 1A (Zellweger)
Amber Amber List (moderate evidence)
PEX2
1 review
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
  • UKGTN
Phenotypes
  • Neonatal and Adult Cholestasis
  • Peroxisome Biogenesis Disorder 5A (Zellweger)
Amber Amber List (moderate evidence)
SERPINA1
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Emory Genetics Laboratory
  • UKGTN
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
  • Alpha-1 Antitrypsin Deficiency
Amber Amber List (moderate evidence)
SLC25A13
2 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Victorian Clinical Genetics Services
  • Emory Genetics Laboratory
  • UKGTN
Phenotypes
  • Neonatal and Adult Cholestasis
  • Citrullinemia type 2, neonatal onset
  • Citrullinemia type 2, adult onset
Red Red List (low evidence)
ABCC2
1 review
1 green
Not set
Sources
  • Victorian Clinical Genetics Services
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
ABCG5
1 review
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
ABCG8
1 review
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
ADK
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
AMACR
1 review
Not set
Sources
  • Victorian Clinical Genetics Services
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
ARG1
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
ATP7B
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
CC2D2A
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
CFTR
1 review
1 green
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
COG7
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
CYP7A1
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
DCDC2
1 review
1 green
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
DGUOK
1 review
1 green
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
DHCR7
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
EHHADH
0 reviews
Not set
Sources
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
EPHX1
0 reviews
BIALLELIC, autosomal or pseudoautosomal
Sources
  • UKGTN
Phenotypes
  • Hypercholanemia, Familial
Red Red List (low evidence)
FAH
1 review
1 green
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
GALT
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
GBA
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
GBE1
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
GPBAR1
0 reviews
Not set
Sources
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
HADHA
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
HAMP
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
HFE
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
HFE2
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
HSD17B4
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
IARS
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
INVS
1 review
1 red
Not set
Sources
  • Victorian Clinical Genetics Services
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
LIPA
1 review
1 green
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
MKS1
1 review
1 green
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
MPI
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
MPV17
1 review
1 green
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
MVK
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
NPHP1
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
NPHP3
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
NPHP4
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
PEX10
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
PEX11B
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
PEX12
1 review
1 red
Not set
Sources
  • Victorian Clinical Genetics Services
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
PEX13
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
PEX14
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
PEX16
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
PEX19
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
PEX26
0 reviews
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
PEX3
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
PEX5
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
PEX6
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
PEX7
0 reviews
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
PKHD1
1 review
1 green
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
POLG
1 review
1 green
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
SCP2
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
SLC10A1
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
SLC10A2
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
SLC27A5
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
SLC30A10
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
SLC40A1
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
SMPD1
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
TALDO1
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
TFR2
0 reviews
Not set
Sources
  • Victorian Clinical Genetics Services
Red Red List (low evidence)
TMEM216
1 review
1 red
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
TRMU
1 review
1 green
Not set
Sources
  • Emory Genetics Laboratory
  • Victorian Clinical Genetics Services
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
UGT1A1
1 review
1 green
Not set
Sources
  • Victorian Clinical Genetics Services
  • Emory Genetics Laboratory
Phenotypes
  • Neonatal and Adult Cholestasis
Red Red List (low evidence)
UTP4
0 reviews
BIALLELIC, autosomal or pseudoautosomal
Sources
  • UKGTN
Phenotypes
  • North American Indian Childhood Cirrhosis

0 STRs

0 reviewed, 0 green

List STR Reviews Mode of inheritance Details
0 STRss

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