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GI tract tumours (Version 1.27)

Level 3: GI tract
Level 2: Tumour syndromes

Relevant disorders: GI tract tumours, Familial colon cancer, Multiple bowel polyps, Peutz-Jeghers syndrome, GI tract, Inherited colorectal cancer (with or without polyposis)
Panel types: Rare Disease 100K
Previous code: 591444928f620348d4b20c16
Description
This panel is NO LONGER ACTIVELY MAINTAINED.

Please use with caution, as the gene list has not been recently updated. Reviews added to this panel are no longer a priority for curation and may not be followed up.

Please consider using an NHS Genomic Medicine Service (GMS) panel instead. The full list of GMS panels can be found here: https://nhsgms-panelapp.genomicsengland.co.uk/panels, with links back to PanelApp should you wish to leave a review on the panel.

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This panel was originally developed for the 100,000 Genomes Project and is still being used for participants in the project, recruited under the following conditions: 
- Familial colon cancer 
- Multiple bowel polyps 
- Peutz-Jeghers syndrome 

For the rare disease eligibility criteria for each condition refer to: https://www.genomicsengland.co.uk/rarediseasecriteria100K

This is a combined panel for GI tract tumour syndrome created on 11th May 2017 by combining the following individual gene panels together:
- Familial colon cancer (code: 137, version 1.5)
- Multiple bowel polyps (code: 14, version 1.9)
- Peutz-Jeghers syndrome (code: 279, version 0.2)

Some of the genes in this panel cause conditions that typically present in adulthood. Please consider this when applying the panel.
Panel Activity

13 reviewers

  • Ellen McDonagh (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Treena Cranston (Oxford)

    Group: NHS Genomic Medicine Centre
    Workplace: NHS diagnostic lab

  • Rachel Robinson (Leeds Genetics Laboratory)

    Group: Other NHS organisation
    Workplace: NHS diagnostic lab

  • Clare Turnbull (Queen Mary University London)

    Group: GeCIP domain
    Workplace: NHS clinical service

  • Ian Tomlinson (University of Oxford)

    Group: GeCIP domain
    Workplace: Research lab

  • Ian Frayling (Cardiff University)

    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

  • Terri McVeigh (Royal Marsden NHS Foundation Trust)

    Group: Other NHS organisation
    Workplace: NHS clinical service

  • Lara Hawkes (Genomics England)

    Group: Other NHS organisation
    Workplace: NHS clinical service

  • Ivone Leong (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Arina Puzriakova (Genomics England Curator)

    Group: Other
    Workplace: Other

  • Claire Palles (University of Birmingham)

    Group: GeCIP domain
    Workplace: Research lab

31 Entities

31 reviewed, 15 green

List Entity Reviews Mode of inheritance Details
31 Entitiess
Green List (high evidence)
APC
7 reviews
4 green 		MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Eligibility statement prior genetic testing
  • Emory Genetics Laboratory
  • Expert list
  • Expert List
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • NHS GMS
  • UKGTN
Phenotypes
  • Adenomatous polyposis coli 175100
  • Brain tumor-polyposis syndrome 2 175100
  • Gardner syndrome 175100
  • Desmoid disease, hereditary 135290
Tags
Green List (high evidence)
BMPR1A
7 reviews
3 green 		MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Eligibility statement prior genetic testing
  • Emory Genetics Laboratory
  • Expert List
  • Expert Review Green
  • NHS GMS
  • Radboud University Medical Center, Nijmegen
  • UKGTN
Phenotypes
  • Gastrointestinal and Colorectal Cancer
  • High Risk Colorectal Cancer
  • juvenile polyposis
  • Polyposis, juvenile intestinal, 174900
  • Polyposis syndrome, hereditary mixed, 2, 610069
  • Juvenile polyposis syndrome, infantile form, 174900
  • Juvenile Polyposis Syndrome
  • Polyposis syndrome, hereditary mixed, 2, 610069
  • Juvenile polyposis syndrome, infantile form, 174900
Tags
Green List (high evidence)
EPCAM
6 reviews
2 green 1 red 		MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Emory Genetics Laboratory
  • Expert Review Green
  • NHS GMS
Phenotypes
  • Colorectal cancer, hereditary nonpolyposis, type 8, OMIM:613244
Tags
  • structural-variant
Green List (high evidence)
MBD4
3 reviews
2 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Literature
Phenotypes
  • Tumor predisposition syndrome 2, OMIM:619975
  • Multi-organ tumour predisposition syndrome
  • Adenomatous colorectal polyposis
  • Colorectal cancer
  • Acute myeloid leukemia
  • Uveal melanoma
Tags
Green List (high evidence)
MLH1
7 reviews
4 green 		BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Emory Genetics Laboratory
  • Expert list
  • Expert List
  • Expert Review Green
  • NHS GMS
Phenotypes
  • Gastrointestinal and Colorectal Cancer
  • High Risk Colorectal Cancer
  • Mismatch repair cancer syndrome 276300 AR
  • Muir-Torre syndrome 158320 AD
Tags
Green List (high evidence)
MSH2
6 reviews
3 green 		BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Emory Genetics Laboratory
  • Expert list
  • Expert List
  • Expert Review Green
  • NHS GMS
Phenotypes
  • Colorectal cancer, hereditary nonpolyposis, type 1 120435 AD
  • Mismatch repair cancer syndrome 276300 AR
  • Muir-Torre syndrome 158320 AD
Tags
Green List (high evidence)
MSH6
5 reviews
3 green 		BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Emory Genetics Laboratory
  • Expert list
  • Expert List
  • Expert Review Green
  • NHS GMS
Phenotypes
  • Colorectal cancer, hereditary nonpolyposis, type 5 614350 AD
  • Endometrial cancer, familial 608089
  • Mismatch repair cancer syndrome 276300 AR
Tags
Green List (high evidence)
MUTYH
5 reviews
3 green 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Emory Genetics Laboratory
  • Expert list
  • Expert List
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • NHS GMS
  • UKGTN
Phenotypes
  • Gastrointestinal and Colorectal Cancer High Risk Adenomas, multiple colorectal 608456
Tags
Green List (high evidence)
NTHL1
7 reviews
2 green 1 red 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert List
  • Expert Review
  • Expert Review Green
  • Literature
  • NHS GMS
  • Research
Phenotypes
  • Familial adenomatous polyposis 3 616415
Tags
Green List (high evidence)
PMS2
5 reviews
3 green 		BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Sources
  • Eligibility statement prior genetic testing
  • Emory Genetics Laboratory
  • Expert List
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Colorectal cancer, hereditary nonpolyposis, type 4 614337
  • Mismatch repair cancer syndrome 276300 AR
Tags
Green List (high evidence)
POLD1
5 reviews
2 green 		MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert list
  • Expert List
  • Expert Review
  • Expert Review Green
  • NHS GMS
Phenotypes
  • {Colorectal cancer, susceptibility to, 10} 612591
Tags
Green List (high evidence)
POLE
5 reviews
2 green 		MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert list
  • Expert List
  • Expert Review
  • Expert Review Green
  • NHS GMS
Phenotypes
  • {Colorectal cancer, susceptibility to, 12} 615083 AD
Tags
Green List (high evidence)
PTEN
6 reviews
3 green 		MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Emory Genetics Laboratory
  • Expert List
  • Expert Review
  • Expert Review Green
  • NHS GMS
Phenotypes
  • PTEN hamartoma tumor syndrome
  • Bannayan-Riley-Ruvalcaba syndrome 153480 AD
  • Cowden syndrome 1 158350
Tags
Green List (high evidence)
SMAD4
6 reviews
3 green 		MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Eligibility statement prior genetic testing
  • Emory Genetics Laboratory
  • Expert List
  • Expert Review Green
  • NHS GMS
  • Radboud University Medical Center, Nijmegen
  • UKGTN
Phenotypes
  • Polyposis, juvenile intestinal, 174900
  • Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome, 175050
Tags
Green List (high evidence)
STK11
7 reviews
3 green 		MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Eligibility statement prior genetic testing
  • Emory Genetics Laboratory
  • Expert List
  • Expert Review Green
  • NHS GMS
  • Other
Phenotypes
  • Peutz-Jeghers syndrome 175200
Tags
Amber List (moderate evidence)
CDH1
3 reviews
1 green 		Not set
Sources
  • Emory Genetics Laboratory
  • Expert Review Amber
Phenotypes
  • Gastrointestinal and Colorectal Cancer
Tags
Red List (low evidence)
ADM
1 review
1 red 		Not set
Sources
  • Expert list
Tags
Red List (low evidence)
BRCA1
2 reviews
2 red 		Not set
Sources
  • Emory Genetics Laboratory
Phenotypes
  • Gastrointestinal and Colorectal Cancer
Tags
Red List (low evidence)
BRCA2
2 reviews
2 red 		Not set
Sources
  • Emory Genetics Laboratory
Phenotypes
  • Gastrointestinal and Colorectal Cancer
Tags
Red List (low evidence)
CDKN2A
1 review
1 red 		Not set
Sources
  • Emory Genetics Laboratory
Phenotypes
  • Gastrointestinal and Colorectal Cancer
Tags
Red List (low evidence)
CHEK2
3 reviews
2 red 		MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Emory Genetics Laboratory
  • Expert Review Red
  • Illumina TruGenome Clinical Sequencing Services
Phenotypes
  • Colorectal cancer
  • Gastrointestinal and Colorectal Cancer
  • High Risk Colorectal Cancer
Tags
Red List (low evidence)
ENG
2 reviews
 MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Red
  • Illumina TruGenome Clinical Sequencing Services
Phenotypes
  • Juvenile Polyposis
Tags
Red List (low evidence)
FOXO3
1 review
1 red 		MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Literature
Phenotypes
  • Hamartomatous polyposis syndromes including Peutz-Jeghers and PTEN hamartoma tumor syndromes
Tags
Red List (low evidence)
GREM1
5 reviews
3 green 		MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Red
  • Literature
  • NHS GMS
  • Radboud University Medical Center, Nijmegen
  • UKGTN
Phenotypes
  • {Colorectal cancer, increased risk, association with}(Peters (2012) Hum Genet 131,217)
  • Oligosyndactyly of the hands, Cenani-Linz-like (Dimitrov (2010) J Med Genet 47,569)
  • Mixed polyposis syndrome (Jaeger (2012) Nat Genet 44,699)
  • Polyposis Syndrome, Hereditary Mixed, 1
  • Hereditary Mixed Polyposis Syndrome
Tags
  • structural-variant
Red List (low evidence)
MSH3
2 reviews
1 green 1 red 		BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Red
  • NHS GMS
  • Research
Tags
Red List (low evidence)
PTPN12
2 reviews
1 red 		Not set
Sources
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Colon cancer
Tags
Red List (low evidence)
RNF43
1 review
1 green 		Not set
Sources
  • NHS GMS
Tags
Red List (low evidence)
SLC26A3
2 reviews
1 red 		Not set
Sources
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • ?Colon cancer (1)
  • Chloride diarrhea, congenital, Finnish type, 214700
Tags
Red List (low evidence)
SMAD9
1 review
1 red 		MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Literature
Phenotypes
  • Hamartomatous Polyposis
  • Gastrointestinal Ganglioneuromas
Tags
Red List (low evidence)
SRC
2 reviews
1 red 		Not set
Sources
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • ?Colon cancer, advanced
Tags
Red List (low evidence)
TP53
1 review
1 red 		Not set
Sources
  • Emory Genetics Laboratory
Phenotypes
  • Gastrointestinal and Colorectal Cancer
  • High Risk Colorectal Cancer
Tags

Major version comments

  • This panel has been formed as a result of merging Familial colon cancer (Version 1.5), Multiple bowel polyps (Version 1.9), Peutz-Jeghers syndrome (Version 0.20) panels and copying the reviews from each panel into this united GI Tract panel

Downloads

Download lists

  • Whole panel
  • Green list (high evidence)
  • Green and Amber Genes
  • Amber Genes
  • Red list (low evidence)

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