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{
"id": 504,
"hash_id": null,
"name": "Inherited polyposis and early onset colorectal cancer - germline testing",
"disease_group": "",
"disease_sub_group": "",
"status": "public",
"version": "2.10",
"version_created": "2023-12-11T15:27:02.596209Z",
"relevant_disorders": [
"Inherited polyposis",
"R211"
],
"stats": {
"number_of_genes": 19,
"number_of_strs": 0,
"number_of_regions": 0
},
"types": [
{
"name": "GMS Rare Disease",
"slug": "gms-rare-disease",
"description": "This panel type is used for GMS panels that are not virtual (i.e. could be a wet lab test)"
},
{
"name": "GMS signed-off",
"slug": "gms-signed-off",
"description": "This panel has undergone review by a NHSE GMS disease specialist group and processes to be signed-off for use within the GMS."
}
],
"genes": [
{
"gene_data": {
"alias": [
"DP2",
"DP3",
"DP2.5",
"PPP1R46"
],
"biotype": "protein_coding",
"hgnc_id": "HGNC:583",
"gene_name": "APC, WNT signaling pathway regulator",
"omim_gene": [
"611731"
],
"alias_name": [
"protein phosphatase 1, regulatory subunit 46"
],
"gene_symbol": "APC",
"hgnc_symbol": "APC",
"hgnc_release": "2017-11-03",
"ensembl_genes": {
"GRch37": {
"82": {
"location": "5:112043195-112181936",
"ensembl_id": "ENSG00000134982"
}
},
"GRch38": {
"90": {
"location": "5:112707498-112846239",
"ensembl_id": "ENSG00000134982"
}
}
},
"hgnc_date_symbol_changed": "1986-01-01"
},
"entity_type": "gene",
"entity_name": "APC",
"confidence_level": "3",
"penetrance": null,
"mode_of_pathogenicity": "",
"publications": [],
"evidence": [
"Expert Review Green",
"NHS GMS",
"Expert List"
],
"phenotypes": [
"Desmoid disease, hereditary, OMIM:135290",
"Brain tumor-polyposis syndrome 2, OMIM:175100",
"Gardner syndrome, OMIM:175100",
"Adenomatous polyposis coli, OMIM:175100",
"Gastric adenocarcinoma and proximal polyposis of the stomach, OMIM:619182"
],
"mode_of_inheritance": "MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown",
"tags": [],
"transcript": null
},
{
"gene_data": {
"alias": [
"ALK3",
"CD292"
],
"biotype": "protein_coding",
"hgnc_id": "HGNC:1076",
"gene_name": "bone morphogenetic protein receptor type 1A",
"omim_gene": [
"601299"
],
"alias_name": null,
"gene_symbol": "BMPR1A",
"hgnc_symbol": "BMPR1A",
"hgnc_release": "2017-11-03",
"ensembl_genes": {
"GRch37": {
"82": {
"location": "10:88516407-88692595",
"ensembl_id": "ENSG00000107779"
}
},
"GRch38": {
"90": {
"location": "10:86756601-86932838",
"ensembl_id": "ENSG00000107779"
}
}
},
"hgnc_date_symbol_changed": "1994-12-12"
},
"entity_type": "gene",
"entity_name": "BMPR1A",
"confidence_level": "3",
"penetrance": null,
"mode_of_pathogenicity": "",
"publications": [],
"evidence": [
"Expert Review Green",
"NHS GMS",
"Expert List"
],
"phenotypes": [
"Polyposis syndrome, hereditary mixed, 2, OMIM:610069",
"Polyposis, juvenile intestinal, OMIM:174900"
],
"mode_of_inheritance": "MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown",
"tags": [],
"transcript": null
},
{
"gene_data": {
"alias": [
"Ly74",
"TROP1",
"GA733-2",
"EGP34",
"EGP40",
"EGP-2",
"KSA",
"CD326",
"Ep-CAM",
"HEA125",
"KS1/4",
"MK-1",
"MH99",
"MOC31",
"323/A3",
"17-1A",
"TACST-1",
"CO-17A",
"ESA"
],
"biotype": "protein_coding",
"hgnc_id": "HGNC:11529",
"gene_name": "epithelial cell adhesion molecule",
"omim_gene": [
"185535"
],
"alias_name": null,
"gene_symbol": "EPCAM",
"hgnc_symbol": "EPCAM",
"hgnc_release": "2017-11-03",
"ensembl_genes": {
"GRch37": {
"82": {
"location": "2:47572297-47614740",
"ensembl_id": "ENSG00000119888"
}
},
"GRch38": {
"90": {
"location": "2:47345158-47387601",
"ensembl_id": "ENSG00000119888"
}
}
},
"hgnc_date_symbol_changed": "2008-12-16"
},
"entity_type": "gene",
"entity_name": "EPCAM",
"confidence_level": "3",
"penetrance": null,
"mode_of_pathogenicity": "",
"publications": [],
"evidence": [
"Expert Review Green",
"NHS GMS"
],
"phenotypes": [
"Colorectal cancer, hereditary nonpolyposis, type 8, OMIM:613244"
],
"mode_of_inheritance": "MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown",
"tags": [],
"transcript": null
},
{
"gene_data": {
"alias": [
"HNPCC",
"FCC2",
"HNPCC2"
],
"biotype": "protein_coding",
"hgnc_id": "HGNC:7127",
"gene_name": "mutL homolog 1",
"omim_gene": [
"120436"
],
"alias_name": null,
"gene_symbol": "MLH1",
"hgnc_symbol": "MLH1",
"hgnc_release": "2017-11-03",
"ensembl_genes": {
"GRch37": {
"82": {
"location": "3:37034823-37107380",
"ensembl_id": "ENSG00000076242"
}
},
"GRch38": {
"90": {
"location": "3:36993332-37050918",
"ensembl_id": "ENSG00000076242"
}
}
},
"hgnc_date_symbol_changed": "1993-11-24"
},
"entity_type": "gene",
"entity_name": "MLH1",
"confidence_level": "3",
"penetrance": null,
"mode_of_pathogenicity": "",
"publications": [],
"evidence": [
"Expert Review Green",
"NHS GMS",
"Expert List"
],
"phenotypes": [
"Colorectal cancer, hereditary nonpolyposis, type 2, OMIM:609310",
"Mismatch repair cancer syndrome, OMIM:276300",
"Muir-Torre syndrome, OMIM:158320"
],
"mode_of_inheritance": "MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown",
"tags": [],
"transcript": null
},
{
"gene_data": {
"alias": [
"HNPCC",
"HNPCC1"
],
"biotype": "protein_coding",
"hgnc_id": "HGNC:7325",
"gene_name": "mutS homolog 2",
"omim_gene": [
"609309"
],
"alias_name": null,
"gene_symbol": "MSH2",
"hgnc_symbol": "MSH2",
"hgnc_release": "2017-11-03",
"ensembl_genes": {
"GRch37": {
"82": {
"location": "2:47630108-47789450",
"ensembl_id": "ENSG00000095002"
}
},
"GRch38": {
"90": {
"location": "2:47402969-47562311",
"ensembl_id": "ENSG00000095002"
}
}
},
"hgnc_date_symbol_changed": "1993-07-28"
},
"entity_type": "gene",
"entity_name": "MSH2",
"confidence_level": "3",
"penetrance": null,
"mode_of_pathogenicity": "",
"publications": [],
"evidence": [
"Expert Review Green",
"NHS GMS",
"Expert List"
],
"phenotypes": [
"Muir-Torre syndrome, OMIM:158320",
"Colorectal cancer, hereditary nonpolyposis, type 1, OMIM:120435",
"Mismatch repair cancer syndrome, OMIM:276300"
],
"mode_of_inheritance": "MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown",
"tags": [],
"transcript": null
},
{
"gene_data": {
"alias": [],
"biotype": "protein_coding",
"hgnc_id": "HGNC:7329",
"gene_name": "mutS homolog 6",
"omim_gene": [
"600678"
],
"alias_name": null,
"gene_symbol": "MSH6",
"hgnc_symbol": "MSH6",
"hgnc_release": "2017-11-03",
"ensembl_genes": {
"GRch37": {
"82": {
"location": "2:47922669-48037240",
"ensembl_id": "ENSG00000116062"
}
},
"GRch38": {
"90": {
"location": "2:47695530-47810101",
"ensembl_id": "ENSG00000116062"
}
}
},
"hgnc_date_symbol_changed": "1995-08-29"
},
"entity_type": "gene",
"entity_name": "MSH6",
"confidence_level": "3",
"penetrance": null,
"mode_of_pathogenicity": "",
"publications": [],
"evidence": [
"Expert Review Green",
"NHS GMS",
"Expert List"
],
"phenotypes": [
"Mismatch repair cancer syndrome, OMIM:276300",
"Colorectal cancer, hereditary nonpolyposis, type 5, OMIM:614350",
"Endometrial cancer, familial, OMIM:608089"
],
"mode_of_inheritance": "MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown",
"tags": [],
"transcript": null
},
{
"gene_data": {
"alias": [
"MYH"
],
"biotype": "protein_coding",
"hgnc_id": "HGNC:7527",
"gene_name": "mutY DNA glycosylase",
"omim_gene": [
"604933"
],
"alias_name": null,
"gene_symbol": "MUTYH",
"hgnc_symbol": "MUTYH",
"hgnc_release": "2017-11-03",
"ensembl_genes": {
"GRch37": {
"82": {
"location": "1:45794835-45806142",
"ensembl_id": "ENSG00000132781"
}
},
"GRch38": {
"90": {
"location": "1:45329163-45340470",
"ensembl_id": "ENSG00000132781"
}
}
},
"hgnc_date_symbol_changed": "1997-10-24"
},
"entity_type": "gene",
"entity_name": "MUTYH",
"confidence_level": "3",
"penetrance": null,
"mode_of_pathogenicity": "",
"publications": [],
"evidence": [
"Expert Review Green",
"NHS GMS",
"Expert List"
],
"phenotypes": [
"Adenomas, multiple colorectal, OMIM:608456"
],
"mode_of_inheritance": "BIALLELIC, autosomal or pseudoautosomal",
"tags": [],
"transcript": null
},
{
"gene_data": {
"alias": [
"NTH1",
"OCTS3"
],
"biotype": "protein_coding",
"hgnc_id": "HGNC:8028",
"gene_name": "nth like DNA glycosylase 1",
"omim_gene": [
"602656"
],
"alias_name": null,
"gene_symbol": "NTHL1",
"hgnc_symbol": "NTHL1",
"hgnc_release": "2017-11-03",
"ensembl_genes": {
"GRch37": {
"82": {
"location": "16:2089816-2097867",
"ensembl_id": "ENSG00000065057"
}
},
"GRch38": {
"90": {
"location": "16:2039815-2047866",
"ensembl_id": "ENSG00000065057"
}
}
},
"hgnc_date_symbol_changed": "1998-05-27"
},
"entity_type": "gene",
"entity_name": "NTHL1",
"confidence_level": "3",
"penetrance": null,
"mode_of_pathogenicity": "",
"publications": [],
"evidence": [
"Expert Review Green",
"NHS GMS",
"Expert List"
],
"phenotypes": [
"Familial adenomatous polyposis 3, OMIM:616415",
"NTHL1-related attenuated familial adenomatous polyposis, MONDO:0014630"
],
"mode_of_inheritance": "BIALLELIC, autosomal or pseudoautosomal",
"tags": [],
"transcript": null
},
{
"gene_data": {
"alias": [
"H_DJ0042M02.9",
"HNPCC4",
"MLH4"
],
"biotype": "protein_coding",
"hgnc_id": "HGNC:9122",
"gene_name": "PMS1 homolog 2, mismatch repair system component",
"omim_gene": [
"600259"
],
"alias_name": null,
"gene_symbol": "PMS2",
"hgnc_symbol": "PMS2",
"hgnc_release": "2017-11-03",
"ensembl_genes": {
"GRch37": {
"82": {
"location": "7:6012870-6048756",
"ensembl_id": "ENSG00000122512"
}
},
"GRch38": {
"90": {
"location": "7:5973239-6009125",
"ensembl_id": "ENSG00000122512"
}
}
},
"hgnc_date_symbol_changed": "1994-12-13"
},
"entity_type": "gene",
"entity_name": "PMS2",
"confidence_level": "3",
"penetrance": null,
"mode_of_pathogenicity": "",
"publications": [],
"evidence": [
"Expert Review Green",
"NHS GMS",
"Expert List"
],
"phenotypes": [
"Colorectal cancer, hereditary nonpolyposis, type 4, OMIM:614337",
"Mismatch repair cancer syndrome 4, OMIM:619101"
],
"mode_of_inheritance": "MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown",
"tags": [],
"transcript": null
},
{
"gene_data": {
"alias": [
"CDC2"
],
"biotype": "protein_coding",
"hgnc_id": "HGNC:9175",
"gene_name": "DNA polymerase delta 1, catalytic subunit",
"omim_gene": [
"174761"
],
"alias_name": [
"CDC2 homolog (S. cerevisiae)"
],
"gene_symbol": "POLD1",
"hgnc_symbol": "POLD1",
"hgnc_release": "2017-11-03",
"ensembl_genes": {
"GRch37": {
"82": {
"location": "19:50887461-50921273",
"ensembl_id": "ENSG00000062822"
}
},
"GRch38": {
"90": {
"location": "19:50384204-50418018",
"ensembl_id": "ENSG00000062822"
}
}
},
"hgnc_date_symbol_changed": "1992-02-06"
},
"entity_type": "gene",
"entity_name": "POLD1",
"confidence_level": "3",
"penetrance": null,
"mode_of_pathogenicity": "",
"publications": [],
"evidence": [
"Expert Review Green",
"NHS GMS",
"Expert List"
],
"phenotypes": [
"{Colorectal cancer, susceptibility to, 10}, OMIM:612591",
"Colorectal cancer, susceptibility to, 10, MONDO:0012953"
],
"mode_of_inheritance": "MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown",
"tags": [],
"transcript": null
},
{
"gene_data": {
"alias": [
"POLE1"
],
"biotype": "protein_coding",
"hgnc_id": "HGNC:9177",
"gene_name": "DNA polymerase epsilon, catalytic subunit",
"omim_gene": [
"174762"
],
"alias_name": [
"DNA polymerase epsilon catalytic subunit A"
],
"gene_symbol": "POLE",
"hgnc_symbol": "POLE",
"hgnc_release": "2017-11-03",
"ensembl_genes": {
"GRch37": {
"82": {
"location": "12:133200348-133263951",
"ensembl_id": "ENSG00000177084"
}
},
"GRch38": {
"90": {
"location": "12:132623753-132687365",
"ensembl_id": "ENSG00000177084"
}
}
},
"hgnc_date_symbol_changed": "1992-02-06"
},
"entity_type": "gene",
"entity_name": "POLE",
"confidence_level": "3",
"penetrance": null,
"mode_of_pathogenicity": "",
"publications": [],
"evidence": [
"Expert Review Green",
"NHS GMS",
"Expert List"
],
"phenotypes": [
"{Colorectal cancer, susceptibility to, 12}, OMIM:615083"
],
"mode_of_inheritance": "MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown",
"tags": [],
"transcript": null
},
{
"gene_data": {
"alias": [
"MMAC1",
"TEP1",
"PTEN1"
],
"biotype": "protein_coding",
"hgnc_id": "HGNC:9588",
"gene_name": "phosphatase and tensin homolog",
"omim_gene": [
"601728"
],
"alias_name": [
"mutated in multiple advanced cancers 1"
],
"gene_symbol": "PTEN",
"hgnc_symbol": "PTEN",
"hgnc_release": "2017-11-03",
"ensembl_genes": {
"GRch37": {
"82": {
"location": "10:89622870-89731687",
"ensembl_id": "ENSG00000171862"
}
},
"GRch38": {
"90": {
"location": "10:87863113-87971930",
"ensembl_id": "ENSG00000171862"
}
}
},
"hgnc_date_symbol_changed": "1997-04-21"
},
"entity_type": "gene",
"entity_name": "PTEN",
"confidence_level": "3",
"penetrance": null,
"mode_of_pathogenicity": "",
"publications": [],
"evidence": [
"Expert Review Green",
"NHS GMS",
"Expert List"
],
"phenotypes": [
"Cowden syndrome 1, OMIM:158350",
"Lhermitte-Duclos syndrome, OMIM:158350",
"Cowden syndrome 1, MONDO:0008021"
],
"mode_of_inheritance": "MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown",
"tags": [],
"transcript": null
},
{
"gene_data": {
"alias": [
"FLJ20315",
"DKFZp781H0392",
"URCC"
],
"biotype": "protein_coding",
"hgnc_id": "HGNC:18505",
"gene_name": "ring finger protein 43",
"omim_gene": [
"612482"
],
"alias_name": null,
"gene_symbol": "RNF43",
"hgnc_symbol": "RNF43",
"hgnc_release": "2017-11-03",
"ensembl_genes": {
"GRch37": {
"82": {
"location": "17:56429861-56494956",
"ensembl_id": "ENSG00000108375"
}
},
"GRch38": {
"90": {
"location": "17:58352500-58417595",
"ensembl_id": "ENSG00000108375"
}
}
},
"hgnc_date_symbol_changed": "2002-04-18"
},
"entity_type": "gene",
"entity_name": "RNF43",
"confidence_level": "3",
"penetrance": null,
"mode_of_pathogenicity": "",
"publications": [
"24512911",
"27081527",
"27329244",
"27582512",
"29330307"
],
"evidence": [
"Expert Review Green",
"NHS GMS"
],
"phenotypes": [
"Sessile serrated polyposis cancer syndrome, OMIM:617108"
],
"mode_of_inheritance": "MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted",
"tags": [],
"transcript": null
},
{
"gene_data": {
"alias": [
"DPC4"
],
"biotype": "protein_coding",
"hgnc_id": "HGNC:6770",
"gene_name": "SMAD family member 4",
"omim_gene": [
"600993"
],
"alias_name": null,
"gene_symbol": "SMAD4",
"hgnc_symbol": "SMAD4",
"hgnc_release": "2017-11-03",
"ensembl_genes": {
"GRch37": {
"82": {
"location": "18:48494410-48611415",
"ensembl_id": "ENSG00000141646"
}
},
"GRch38": {
"90": {
"location": "18:51028394-51085045",
"ensembl_id": "ENSG00000141646"
}
}
},
"hgnc_date_symbol_changed": "2004-05-26"
},
"entity_type": "gene",
"entity_name": "SMAD4",
"confidence_level": "3",
"penetrance": null,
"mode_of_pathogenicity": "",
"publications": [],
"evidence": [
"Expert Review Green",
"NHS GMS",
"Expert List"
],
"phenotypes": [
"Polyposis, juvenile intestinal, OMIM:174900",
"Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome, OMIM:175050"
],
"mode_of_inheritance": "MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown",
"tags": [],
"transcript": null
},
{
"gene_data": {
"alias": [
"PJS",
"LKB1"
],
"biotype": "protein_coding",
"hgnc_id": "HGNC:11389",
"gene_name": "serine/threonine kinase 11",
"omim_gene": [
"602216"
],
"alias_name": [
"polarization-related protein LKB1"
],
"gene_symbol": "STK11",
"hgnc_symbol": "STK11",
"hgnc_release": "2017-11-03",
"ensembl_genes": {
"GRch37": {
"82": {
"location": "19:1189406-1228428",
"ensembl_id": "ENSG00000118046"
}
},
"GRch38": {
"90": {
"location": "19:1177558-1228435",
"ensembl_id": "ENSG00000118046"
}
}
},
"hgnc_date_symbol_changed": "1998-01-21"
},
"entity_type": "gene",
"entity_name": "STK11",
"confidence_level": "3",
"penetrance": null,
"mode_of_pathogenicity": "",
"publications": [],
"evidence": [
"Expert Review Green",
"NHS GMS",
"Expert List"
],
"phenotypes": [
"Peutz-Jeghers syndrome, OMIM:175200",
"Peutz-Jeghers syndrome, MONDO:0008280"
],
"mode_of_inheritance": "MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown",
"tags": [],
"transcript": null
},
{
"gene_data": {
"alias": [
"MGC126582",
"DKFZp781B0869"
],
"biotype": "protein_coding",
"hgnc_id": "HGNC:904",
"gene_name": "axin 2",
"omim_gene": [
"604025"
],
"alias_name": [
"conductin",
"axil"
],
"gene_symbol": "AXIN2",
"hgnc_symbol": "AXIN2",
"hgnc_release": "2017-11-03",
"ensembl_genes": {
"GRch37": {
"82": {
"location": "17:63524681-63557765",
"ensembl_id": "ENSG00000168646"
}
},
"GRch38": {
"90": {
"location": "17:65528563-65561647",
"ensembl_id": "ENSG00000168646"
}
}
},
"hgnc_date_symbol_changed": "1998-09-17"
},
"entity_type": "gene",
"entity_name": "AXIN2",
"confidence_level": "2",
"penetrance": null,
"mode_of_pathogenicity": null,
"publications": [
"15042511",
"21416598",
"30671715",
"32807118",
"34637023"
],
"evidence": [
"Expert Review Amber",
"Literature"
],
"phenotypes": [
"Oligodontia-colorectal cancer syndrome, OMIM:608615"
],
"mode_of_inheritance": "MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted",
"tags": [],
"transcript": []
},
{
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}
},
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"9024286",
"10092300",
"12696020",
"18084292",
"21128281",
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},
{
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},
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},
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"Expert Review Amber",
"Literature"
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"Adenomatous colorectal polyposis",
"Colorectal cancer",
"Acute myeloid leukemia",
"Uveal melanoma"
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},
{
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"Mismatch repair protein 1"
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"82": {
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},
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}
},
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}
],
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}