Description
This panel is used for clinical indication 'R171 Cholestasis' in the NHS Genomic Medicine Service.

Further information on the testing criteria and any overlapping clinical indications can be found within (https://www.england.nhs.uk/publication/national-genomic-test-directories/) under 'R171 Cholestasis'.

The content of this panel (version 1.21: https://panelapp.genomicsengland.co.uk/api/v1/panels/544/?version=1.21) was signed off under NHS Genomic Medicine Service governance on (20/08/2020).

This panel will continue to be curated based on external reviews and Genomics England curation. New changes will be reflected in an increase to the minor version of the panel and details of these can be viewed in the 'Panel Activity' page. Periodically, these changes will be reviewed by a NHS Genomic Medicine Service evaluation process.  The content that is agreed for the GMS panels will be reflected in an updated version number. 

CNVs, STRs and genes encoded by the mitochondrial genome may not be routinely included in the analysis where the panel is NOT delivered by WGS. Please contact your Genomic Laboratory Hub for information regarding specific queries.

15 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

  • Miranda Durkie (Genetics)

    Group: GeCIP domain
    Workplace: NHS diagnostic lab

  • Ellen Thomas (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Sarah Leigh (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Rebecca Foulger (Genomics England curator)

    Group: Other
    Workplace: Other

  • Louise Daugherty (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Helen Brittain (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Bill Griffiths (Cambridge University Hospitals)

    Group: NHS Genomic Medicine Centre
    Workplace: NHS clinical service

  • Eleanor Williams (Genomics England Curator)

    Group: Other
    Workplace: Other

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

    Group: Other NHS organisation
    Workplace: NHS clinical service

  • Zornitza Stark (Australian Genomics)

    Group: Other
    Workplace: Other clinical service

  • Anna de Burca (Genomics England Curator)

    Group: NHS Genomic Medicine Centre
    Workplace: NHS clinical service

  • Ivone Leong (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Arina Puzriakova (Genomics England Curator)

    Group: Other
    Workplace: Other

60 Entities

60 reviewed, 32 green

List Entity Reviews Mode of inheritance Details
60 Entitiess
Green Green List (high evidence)
ABCB11
3 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Familial Intrahepatic Cholestasis
  • Cholestasis, progressive familial intrahepatic 2, 601847
  • Cholestasis, Progressive Familial Intrahepatic 2
  • PFIC2
  • Cholestasis, benign recurrent intrahepatic, 2, 605479
  • Neonatal and Adult Cholestasis
Tags
Green Green List (high evidence)
ABCB4
4 reviews
3 green
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Progressive Familial Intrahepatic Cholestasis
  • modifier in other forms of genetic cholestasis
  • Familial Intrahepatic Cholestasis
  • gallstones
  • cholelithiasis
  • PFIC
  • PFIC3
  • Cholestasis, progressive familial intrahepatic 3, 602347
  • Cholestasis, intrahepatic, of pregnancy, 3, 614972
  • Neonatal and Adult Cholestasis
  • Cholestasis, Progressive Familial Intrahepatic 3
Tags
Green Green List (high evidence)
ABCC2
4 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Emory Genetics Laboratory
  • Expert Review Green
  • NHS GMS
  • Other
  • Victorian Clinical Genetics Services
Phenotypes
  • modifier in biliary atresia
  • Dubin Johnson syndrome
  • Cholestasis
  • intrahepatic cholestasis of pregnancy
  • Dubin-Johnson syndrome, 237500
Tags
Green Green List (high evidence)
AKR1D1
4 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Emory Genetics Laboratory
  • Expert Review Green
  • NHS GMS
  • Other
  • UKGTN
  • Victorian Clinical Genetics Services
Phenotypes
  • Bile acid synthesis defect, congenital, 2 235555
  • fat soluble vitamin deficiency
  • liver failure
  • bile salt synthesis defect
  • Bile acid synthesis defect, congenital, 2
  • Neonatal and Adult Cholestasis
  • cholestasis
Tags
Green Green List (high evidence)
ALDOB
4 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Emory Genetics Laboratory
  • Expert Review Green
  • NHS GMS
  • Other
  • UKGTN
  • Victorian Clinical Genetics Services
Phenotypes
  • acute liver failure
  • Neonatal and Adult Cholestasis
  • Fructose intolerance, hereditary
Tags
Green Green List (high evidence)
AMACR
4 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Neonatal and Adult Cholestasis
  • Bile acid synthesis defect, congenital, 4 214950
Tags
Green Green List (high evidence)
ATP8B1
4 reviews
3 green
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Familial Intrahepatic Cholestasis
  • Cholestasis, intrahepatic, of pregnancy, 1, 147480
  • Cholestasis, Progressive Familial Intrahepatic 1
  • Cholestasis, benign recurrent intrahepatic, 243300
  • Cholestasis, progressive familial intrahepatic 1, 211600
  • Neonatal and Adult Cholestasis
Tags
Green Green List (high evidence)
BAAT
3 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Hypercholanemia, Familial
  • fat soluble vitamin deficiency
  • Hypercholanemia, familial, 607748
  • cholestasis
  • Neonatal and Adult Cholestasis
Tags
Green Green List (high evidence)
BCS1L
4 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
  • Expert Review Amber
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Cholestasis
  • GRACILE syndrome
Tags
Green Green List (high evidence)
CLDN1
3 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • ichthyosis-hypotrichosis-sclerosing cholangitis
  • Ichthyosis, leukocyte vacuoles, alopecia and sclerosing cholangitis, 607626
  • Neonatal and Adult Cholestasis
  • NISCH syndrome
  • Neonatal ichthyosis sclerosing cholangitis (NISCH) syndrome
Tags
Green Green List (high evidence)
CYP27A1
4 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Emory Genetics Laboratory
  • Expert Review Green
  • NHS GMS
  • Other
  • UKGTN
  • Victorian Clinical Genetics Services
Phenotypes
  • Severe neonatal cholestasis
  • Cerebrotendinous xanthomatosis, 213700
Tags
Green Green List (high evidence)
CYP7A1
5 reviews
1 green 2 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Expert Review Red
  • NHS GMS
  • Other
Phenotypes
  • Bile acid synthesis defect, congenital, 3
  • Neonatal and Adult Cholestasis
Tags
Green Green List (high evidence)
DCDC2
4 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Emory Genetics Laboratory
  • Expert Review Green
  • NHS GMS
  • Other
  • Victorian Clinical Genetics Services
Phenotypes
  • Sclerosing cholangitis, neonatal, 617394
  • PFIC type 5
  • Neonatal sclerosis cholangitis
  • Neonatal and Adult Cholestasis
Tags
Green Green List (high evidence)
FAH
3 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
Phenotypes
  • Neonatal and Adult Cholestasis
  • Tyrosinaemia, Type 1, 276700
  • Cholestasis
Tags
Green Green List (high evidence)
HSD3B7
3 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Bile acid sythesis defect, congenital, 1 607765
  • Neonatal and Adult Cholestasis
Tags
Green Green List (high evidence)
JAG1
6 reviews
4 green
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Alagille syndrome
  • Neonatal and Adult Cholestasis
  • Alagille syndrome 1, 118450
Tags
Green Green List (high evidence)
MYO5B
4 reviews
2 green 1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
  • Expert Review Green
  • NHS GMS
Phenotypes
  • Microvillus inclusion disease, 251850
  • Cholestasis
  • MYO5B associated disease
Tags
Green Green List (high evidence)
NOTCH2
5 reviews
3 green
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Alagille syndrome 2
  • Neonatal and Adult Cholestasis
Tags
Green Green List (high evidence)
NPC1
4 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Niemann-Pick disease, type D, 257220
  • Niemann-Pick disease type C1, 257220
  • Neonatal and Adult Cholestasis
Tags
Green Green List (high evidence)
NPC2
4 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Neonatal and Adult Cholestasis
  • Niemann-Pick disease type C2, 607625
Tags
Green Green List (high evidence)
NR1H4
4 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • ciliopathy
  • Cholestasis, Progressive Familial Intrahepatic 5
  • modifier of other genetic cholestatic conditions
  • Neonatal and Adult Cholestasis
  • Cholestasis, progressive familial intrahepatic 5, 617049
Tags
Green Green List (high evidence)
PEX1
5 reviews
1 green 1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Peroxisome Biogenesis Disorder 1A (Zellweger), 214100
  • Zellweger syndrome
  • Neonatal and Adult Cholestasis
Tags
Green Green List (high evidence)
PEX12
3 reviews
1 green 1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Peroxisome biogenesis disorder 3B 266510
  • Peroxisome biogenesis disorder 3A (Zellweger) 614859
Tags
Green Green List (high evidence)
PEX26
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Peroxisome biogenesis disorder 7A (Zellweger)614872
Tags
Green Green List (high evidence)
PEX6
3 reviews
1 green 1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Peroxisome biogenesis disorder 4A (Zellweger) 614862
Tags
Green Green List (high evidence)
SERPINA1
5 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Alpha-1 Antitrypsin Deficiency
  • Neonatal and Adult Cholestasis
Tags
Green Green List (high evidence)
SLC25A13
4 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • CHOLESTASIS, NEONATAL INTRAHEPATIC, CAUSED BY CITRIN DEFICIENCY
  • NICCD
  • Citrullinemia type 2, neonatal onset
  • Citrullinemia type 2, adult onset
  • Citrullinemia, adult-onset type II 603471
  • Citrullinemia, type II, neonatal-onset 605814
  • Neonatal and Adult Cholestasis
Tags
Green Green List (high evidence)
TALDO1
4 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Transaldolase deficiency, 606003
Tags
Green Green List (high evidence)
TJP2
3 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Cholestasis, Progressive Familial Intrahepatic 4
  • Neonatal and Adult Cholestasis
  • Cholestasis, progressive familial intrahepatic 4, 615878
Tags
Green Green List (high evidence)
UGT1A1
3 reviews
2 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • [Gilbert syndrome] 143500
  • Crigler-Najjar syndrome, type I 218800
  • Neonatal and Adult Cholestasis
  • Crigler-Najjar syndrome, type II 606785
  • unconjugated jaundice
Tags
Green Green List (high evidence)
VIPAS39
3 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Arthrogryposis, Renal Dysfunction, and Cholestasis 2
  • ARC syndrome
  • Arthrogryposis-renal-cholestasis syndrome
  • Neonatal and Adult Cholestasis
  • Arthrogryposis, renal dysfunction, and cholestasis 2, 613404
Tags
Green Green List (high evidence)
VPS33B
4 reviews
3 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • arthrogryposis-renal-cholestasis syndrome
  • Arthrogryposis, renal dysfunction, and cholestasis 1, 208085
  • Arthrogryposis, Renal Dysfunction, and Cholestasis 1
  • Arthrogryposis, Renal Dysfunction, and Cholestasis Syndrome
  • ARC syndrome
  • Neonatal and Adult Cholestasis
  • Arthrogryposis, Renal Dysfunction, And Cholestasis 1
Tags
Amber Amber List (moderate evidence)
CYP7B1
5 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Emory Genetics Laboratory
  • Expert Review Amber
  • NHS GMS
  • Other
  • UKGTN
  • Victorian Clinical Genetics Services
Phenotypes
  • Bile acid synthesis defect, congenital, 3
  • Neonatal and Adult Cholestasis
Tags
Amber Amber List (moderate evidence)
FARSB
1 review
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • Rajab interstitial lung disease with brain calcifications, 613658
Tags
Amber Amber List (moderate evidence)
GNAS
3 reviews
1 green
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert list
  • Expert Review Amber
  • NHS GMS
  • Other
Phenotypes
  • McCune-Albright syndrome
  • Cholestasis
Tags
Amber Amber List (moderate evidence)
KIF12
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • Cholestasis
  • High Gamma-Glutamyltransferase (GGT)
Tags
  • for-review
Amber Amber List (moderate evidence)
LSR
2 reviews
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • transient neonatal cholestasis
  • intellectual disability
  • short stature
Tags
  • watchlist
Amber Amber List (moderate evidence)
NBAS
2 reviews
1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • Infantile liver failure syndrome 2, 616483
Tags
  • for-review
Amber Amber List (moderate evidence)
PEX14
2 reviews
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
  • Expert Review Amber
Phenotypes
  • Peroxisome biogenesis disorder 13A (Zellweger), 614887
Tags
Amber Amber List (moderate evidence)
PEX2
3 reviews
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Neonatal and Adult Cholestasis
  • Peroxisome Biogenesis Disorder 5A (Zellweger), 614866
Tags
Amber Amber List (moderate evidence)
UNC45A
2 reviews
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
  • Expert Review Amber
Phenotypes
  • Cholestasis
  • Diarrhoea
  • Bone fragility
  • Impaired hearing
Tags
  • for-review
Amber Amber List (moderate evidence)
USP53
3 reviews
2 green 1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • NHS GMS
Phenotypes
  • Paediatric cholestatic liver disease
  • Cholestasis
  • deafness
Tags
  • for-review
Amber Amber List (moderate evidence)
YARS
1 review
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • Charcot-Marie-Tooth disease, dominant intermediate C 608323
  • Intellectual disability
  • deafness
  • nystagmus
  • liver dysfunction
Tags
  • for-review
  • new-gene-name
  • watchlist
Amber Amber List (moderate evidence)
ZFYVE19
1 review
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • Cholestasis
Tags
  • for-review
Red Red List (low evidence)
PPM1F
2 reviews
1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Red
  • Literature
Phenotypes
  • sclerosing cholangitis
  • short stature
  • hypothyroidism
  • abnormal tongue pigmentation
Tags
Red Red List (low evidence)
WDR83OS
2 reviews
1 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Red
  • Literature
Phenotypes
  • Cholestasis
Tags
No list No list
ATP7B
1 review
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
Phenotypes
  • Wilson disease, MIM# 277900
Tags
No list No list
CC2D2A
5 reviews
1 green 2 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Removed
  • NHS GMS
  • Other
Phenotypes
  • COACH syndrome 216360
  • Meckel syndrome 6 612284
  • Joubert syndrome 9 612285
  • Congenital hepatic fibrosis
  • Ciliopathy
Tags
  • for-review
No list No list
COG7
1 review
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
Phenotypes
  • Congenital disorder of glycosylation, type IIe , MIM#608779
Tags
No list No list
DGUOK
1 review
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
Phenotypes
  • Mitochondrial DNA depletion syndrome 3 (hepatocerebral type), MIM# 251880
Tags
No list No list
GALM
1 review
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Literature
Phenotypes
  • Galactosemia IV, 618881
Tags
No list No list
GALT
1 review
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
Phenotypes
  • Galactosemia, MIM# 230400
Tags
No list No list
GBA
1 review
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
Phenotypes
  • Gaucher disease
Tags
No list No list
HNF1B
1 review
1 green
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert list
Phenotypes
  • Renal cysts and diabetes syndrome, MIM# 137920
Tags
No list No list
IARS
1 review
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
Phenotypes
  • Growth retardation, impaired intellectual development, hypotonia, and hepatopathy, MIM#617093
Tags
No list No list
MPV17
1 review
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
Phenotypes
  • Mitochondrial DNA depletion syndrome 6 (hepatocerebral type), 256810
Tags
No list No list
NPHP3
1 review
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
Phenotypes
  • Renal-hepatic-pancreatic dysplasia 1, 208540
Tags
No list No list
PKHD1
1 review
1 green
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert list
Phenotypes
  • Polycystic kidney disease 4, with or without hepatic disease, 263200
Tags
No list No list
RPGRIP1L
4 reviews
1 green 2 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Emory Genetics Laboratory
  • Expert list
  • Expert Review Removed
  • Illumina TruGenome Clinical Sequencing Services
  • NHS GMS
  • Radboud University Medical Center, Nijmegen
  • UKGTN
Phenotypes
  • Meckel syndrome 5 (611561)
  • Joubert syndrome 7 (611560)
  • COACH syndrome (216360)
  • Congenital hepatic fibrosis
Tags
  • for-review
No list No list
TMEM67
4 reviews
2 green 2 red
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Emory Genetics Laboratory
  • Expert list
  • Expert Review Removed
  • Illumina TruGenome Clinical Sequencing Services
  • NHS GMS
  • Radboud University Medical Center, Nijmegen
  • UKGTN
Phenotypes
  • COACH syndrome (216360)
  • {Bardet-Biedl syndrome 14, modifier of} (615991)
  • Nephronophthisis 11 (613550)
  • Meckel syndrome 3 (607361)
  • Joubert syndrome 6 (310688)
  • congenital hepatic fibrosis
Tags

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