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feat: build output files for background data containers (#35) (#41)
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‎Snakefile

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@@ -29,6 +29,9 @@ if os.environ.get("CI", "false").lower() == "true":
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cwd = os.getcwd()
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old_path = os.environ["PATH"]
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os.environ["PATH"] = f"{cwd}/test-mode-bin:{old_path}"
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RUNS_IN_CI = True
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else:
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RUNS_IN_CI = False
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# ===============================================================================================
@@ -71,7 +74,6 @@ rule all:
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f"work/genes/entrez/{DV.today}/gene_info.jsonl",
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f"work/genes/gnomad/{DV.gnomad_constraints}/gnomad_constraints.tsv",
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f"work/genes/hgnc/{DV.today}/hgnc_info.jsonl",
74-
f"work/genes/hgnc/{DV.today}/hgnc_xlink.tsv",
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f"work/genes/mim2gene/{DV.today}/mim2gene.tsv",
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# reference-specific annotations
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# -- background/population sequence variants and annotations thereof
@@ -96,38 +98,16 @@ rule all:
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f"work/annos/grch38/seqvars/gnomad_mtdna/{DV.gnomad_mtdna}/gnomad_mtdna.vcf.gz",
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f"work/download/annos/grch38/seqvars/gnomad_exomes/{DV.gnomad_v2}/.done",
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f"work/download/annos/grch38/seqvars/gnomad_genomes/{DV.gnomad_v3}/.done",
99-
# -- background/population structural variants and annoations thereof
100-
# ---- GRCh37
101-
f"work/annos/grch37/strucvars/dbvar/{DV.dbvar}/dbvar.bed.gz",
102-
f"work/annos/grch37/strucvars/dgv/{DV.dgv}/dgv.bed.gz",
103-
f"work/annos/grch37/strucvars/dgv_gs/{DV.dgv_gs}/dgv_gs.bed.gz",
104-
f"work/annos/grch37/strucvars/exac/{DV.exac_cnv}/exac.bed.gz",
105-
f"work/annos/grch37/strucvars/g1k/{DV.g1k_svs}/g1k.bed.gz",
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f"work/annos/grch37/strucvars/gnomad/{DV.gnomad_sv}/gnomad_sv.bed.gz",
107-
# ---- GRCh38
108-
f"work/annos/grch38/strucvars/dbvar/{DV.dbvar}/dbvar.bed.gz",
109-
f"work/annos/grch38/strucvars/dgv/{DV.dgv}/dgv.bed.gz",
110-
f"work/annos/grch38/strucvars/dgv_gs/{DV.dgv_gs}/dgv_gs.bed.gz",
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# NB: gnomAD-SV GRCh38 was announced end of 2020 but not released yet
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# -- genome browser "features" (position-specific)
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# ---- GRCh37
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f"work/annos/grch37/features/cons/{DV.ucsc_cons_37}/ucsc_conservation.tsv",
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f"work/annos/grch37/features/ensembl/{DV.ensembl_37}/ensembl_genes.bed.gz",
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f"work/annos/grch37/features/refseq/{DV.refseq_37}/refseq_genes.bed.gz",
117-
"work/annos/grch37/features/tads/dixon2015/hesc.bed",
118-
f"work/annos/grch37/features/ucsc/{DV.ucsc_genomic_super_dups_37}/genomicSuperDups.bed.gz",
119-
f"work/annos/grch37/features/ucsc/{DV.ucsc_rmsk_37}/rmsk.bed.gz",
120-
f"work/annos/grch37/features/ucsc/{DV.ucsc_alt_seq_liftover_37}/altSeqLiftOverPsl.bed.gz",
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f"work/annos/grch37/features/ucsc/{DV.ucsc_fix_seq_liftover_37}/fixSeqLiftOverPsl.bed.gz",
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# ---- GRCh38
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f"work/annos/grch38/features/cons/{DV.ucsc_cons_38}/ucsc_conservation.tsv",
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f"work/annos/grch38/features/ensembl/{DV.ensembl_38}/ensembl_genes.bed.gz",
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f"work/annos/grch38/features/refseq/{DV.refseq_38}/refseq_genes.bed.gz",
126-
"work/annos/grch38/features/tads/dixon2015/hesc.bed",
127-
f"work/annos/grch38/features/ucsc/{DV.ucsc_genomic_super_dups_38}/genomicSuperDups.bed.gz",
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f"work/annos/grch38/features/ucsc/{DV.ucsc_rmsk_38}/rmsk.bed.gz",
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f"work/annos/grch38/features/ucsc/{DV.ucsc_alt_seq_liftover_38}/altSeqLiftOverPsl.bed.gz",
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f"work/annos/grch38/features/ucsc/{DV.ucsc_fix_seq_liftover_38}/fixSeqLiftOverPsl.bed.gz",
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#
132112
# == output directory ===================================================================
133113
#
@@ -165,6 +145,41 @@ rule all:
165145
# ---- UCSC conservation
166146
f"output/worker/annos/seqvars/cons-grch37-{DV.ucsc_cons_37}+{PV.annonars}/rocksdb/IDENTITY",
167147
f"output/worker/annos/seqvars/cons-grch38-{DV.ucsc_cons_38}+{PV.annonars}/rocksdb/IDENTITY",
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# ----- Genes
149+
f"output/worker/genes-{DV.acmg_sf}+{DV.gnomad_constraints}+{DV.dbnsfp}+{DV.today}+{PV.worker}/rocksdb/IDENTITY",
150+
f"output/worker/genes-xlink-{DV.today}/genes-xlink.tsv",
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f"output/worker/genes-txs-grch37-{DV.mehari_tx}/mehari-data-txs-grch37-{DV.mehari_tx}.bin.zst",
152+
f"output/worker/genes-txs-grch38-{DV.mehari_tx}/mehari-data-txs-grch38-{DV.mehari_tx}.bin.zst",
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# ----- HPO
154+
f"output/viguno/hpo-{DV.hpo}+{PV.viguno}/hp.obo",
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f"output/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype.hpoa",
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f"output/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype_to_genes.txt",
157+
f"output/viguno/hpo-{DV.hpo}+{PV.viguno}/hpo.bin",
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# ----- background/population structural variants and annotations thereof
159+
f"output/worker/annos/strucvars/dbvar-grch37-{DV.dbvar}/dbvar.bed.gz",
160+
f"output/worker/annos/strucvars/dbvar-grch38-{DV.dbvar}/dbvar.bed.gz",
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f"output/worker/annos/strucvars/dgv-grch37-{DV.dgv}/dgv.bed.gz",
162+
f"output/worker/annos/strucvars/dgv-grch38-{DV.dgv}/dgv.bed.gz",
163+
f"output/worker/annos/strucvars/dgv-gs-grch37-{DV.dgv_gs}/dgv-gs.bed.gz",
164+
f"output/worker/annos/strucvars/dgv-gs-grch38-{DV.dgv_gs}/dgv-gs.bed.gz",
165+
f"output/worker/annos/strucvars/exac-grch37-{DV.exac_cnv}/exac.bed.gz",
166+
f"output/worker/annos/strucvars/g1k-grch37-{DV.g1k_svs}/g1k.bed.gz",
167+
f"output/worker/annos/strucvars/gnomad-grch37-{DV.gnomad_sv}/gnomad.bed.gz",
168+
# ----- known pathogenic MMS
169+
f"output/worker/annos/strucvars/patho-mms-grch37-{DV.patho_mms}/patho-mms.bed",
170+
f"output/worker/annos/strucvars/patho-mms-grch38-{DV.patho_mms}/patho-mms.bed",
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# ----- problematic regions (rmsk, genomicSuperDups, altSeqLiftOverPsl, fixSeqLiftOverPsl)
172+
f"output/worker/annos/features/ucsc-genomicsuperdups-grch37-{DV.ucsc_genomic_super_dups_37}/genomicSuperDups.bed.gz",
173+
f"output/worker/annos/features/ucsc-genomicsuperdups-grch38-{DV.ucsc_genomic_super_dups_38}/genomicSuperDups.bed.gz",
174+
f"output/worker/annos/features/ucsc-rmsk-grch37-{DV.ucsc_rmsk_37}/rmsk.bed.gz",
175+
f"output/worker/annos/features/ucsc-rmsk-grch38-{DV.ucsc_rmsk_38}/rmsk.bed.gz",
176+
f"output/worker/annos/features/ucsc-altseqliftoverpsl-grch37-{DV.ucsc_alt_seq_liftover_37}/altSeqLiftOverPsl.bed.gz",
177+
f"output/worker/annos/features/ucsc-altseqliftoverpsl-grch38-{DV.ucsc_alt_seq_liftover_38}/altSeqLiftOverPsl.bed.gz",
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f"output/worker/annos/features/ucsc-fixseqliftoverpsl-grch37-{DV.ucsc_fix_seq_liftover_37}/fixSeqLiftOverPsl.bed.gz",
179+
f"output/worker/annos/features/ucsc-fixseqliftoverpsl-grch38-{DV.ucsc_fix_seq_liftover_38}/fixSeqLiftOverPsl.bed.gz",
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# ----- tads
181+
"output/worker/annos/strucvars/tads-grch37-dixon2015/hesc.bed",
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"output/worker/annos/strucvars/tads-grch38-dixon2015/hesc.bed",
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169184

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# ===============================================================================================
@@ -173,11 +188,14 @@ rule all:
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174189

175190
# -- work directory -----------------------------------------------------------------------------
191+
# Misc rules.
192+
include: "rules/work/misc/hpo.smk"
176193
# Gene-related rules.
177194
include: "rules/work/genes/dbnsfp.smk"
178195
include: "rules/work/genes/ensembl.smk"
179196
include: "rules/work/genes/gnomad.smk"
180197
include: "rules/work/genes/hgnc.smk"
198+
include: "rules/work/genes/mehari_data_tx.smk"
181199
include: "rules/work/genes/ncbi.smk"
182200
# Reference sequence--related rules.
183201
include: "rules/work/reference/human.smk"
@@ -202,13 +220,21 @@ include: "rules/work/annos/strucvars/exac.smk"
202220
include: "rules/work/annos/strucvars/g1k.smk"
203221
include: "rules/work/annos/strucvars/gnomad.smk"
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# -- output directory ---------------------------------------------------------------------------
223+
# ---- mehari
205224
include: "rules/output/mehari/freqs.smk"
206-
include: "rules/output/worker/cadd.smk"
207-
include: "rules/output/worker/dbsnp.smk"
208-
include: "rules/output/worker/dbnsfp.smk"
209-
include: "rules/output/worker/dbscsnv.smk"
210-
include: "rules/output/worker/gnomad_mtdna.smk"
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include: "rules/output/worker/gnomad_exomes.smk"
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include: "rules/output/worker/gnomad_genomes.smk"
213-
include: "rules/output/worker/helix.smk"
214-
include: "rules/output/worker/cons.smk"
225+
# ---- viguno
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include: "rules/output/viguno/hpo.smk"
227+
# ------ annonars
228+
include: "rules/output/annonars/cadd.smk"
229+
include: "rules/output/annonars/cons.smk"
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include: "rules/output/annonars/dbnsfp.smk"
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include: "rules/output/annonars/dbscsnv.smk"
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include: "rules/output/annonars/dbsnp.smk"
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include: "rules/output/annonars/gnomad_exomes.smk"
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include: "rules/output/annonars/gnomad_genomes.smk"
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include: "rules/output/annonars/gnomad_mtdna.smk"
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include: "rules/output/annonars/helix.smk"
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# ---- worker
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# ------ global
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include: "rules/output/worker/genes.smk"
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include: "rules/output/worker/patho_mms.smk"

‎data/acmg/3.1/acmg.spec.json

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@@ -0,0 +1,21 @@
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{
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"dc:format": "text/tsv",
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"dc:identifier": "gene-centric/acmg/acmg-sf-genes.tsv:3.1",
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"dc:title": "ACMG Secondary Findings Gene List (v3.1)",
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"dc:description": "This is version 3.1 of the ACMG gene list for reporting incidental findings. The file was curated from PMID:35802134 as gene symbols and then translated to ENSEMBL and Entrez/NCBI gene ID with the HGNC BioMart",
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"dc:created": "2022-02-03",
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"dc:creator": "American College of Medical Genetics",
8+
"dc:contributor": [
9+
"VarFish Developer Team"
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],
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"dc:source": [
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"PMID:35802134",
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"https://www.ncbi.nlm.nih.gov/clinvar/docs/acmg/",
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"https://biomart.genenames.org/"
15+
],
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"tsv:columns": {
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"gene_symbol": "HGNC approve gene symbol",
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"ensembl_gene_id": "ENSEMBL gene ID",
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"entrez_gene_id": "Entrez/NCBI gene ID"
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}
21+
}

‎data/acmg/3.1/acmg.tsv

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hgnc_id ensembl_gene_id ncbi_gene_id gene_symbol mim_gene_id disease_phenotype disorder_mim phenotype_category inheritance sf_list_version variants_to_report
2+
HGNC:130 ENSG00000107796 59 ACTA2 102620 Familial thoracic aortic aneurysm 611788 Cardiovascular AD 1.0 All P and LP
3+
HGNC:143 ENSG00000159251 70 ACTC1 102540 Hypertrophic cardiomyopathy 612098 Cardiovascular AD 1.0 All P and LP
4+
HGNC:175 ENSG00000139567 94 ACVRL1 601284 Hereditary hemorrhagic telangiectasia 600376 Miscellaneous AD 3.0 All P and LP
5+
HGNC:583 ENSG00000134982 324 APC 611731 Familial adenomatous polyposis 175100 Cancer AD 1.0 All P and LP
6+
HGNC:603 ENSG00000084674 338 APOB 107730 Familial hypercholesterolemia 144010 Cardiovascular AD 1.0 All P and LP
7+
HGNC:870 ENSG00000123191 540 ATP7B 606882 Wilson disease 277900 Miscellaneous AR 2.0 P and LP (2 variants)
8+
HGNC:939 ENSG00000151929 9531 BAG3 603883 Dilated cardiomyopathy 613881 Cardiovascular AD 3.1 All P and LP
9+
HGNC:939 ENSG00000151929 9531 BAG3 603883 Myofibrillar myopathy 612954 Cardiovascular AD 3.1 All P and LP
10+
HGNC:1076 ENSG00000107779 657 BMPR1A 601299 Juvenile polyposis syndrome 174900 Cancer AD 1.0 All P and LP
11+
HGNC:1100 ENSG00000012048 672 BRCA1 113705 Hereditary breast and ovarian cancer 604370 Cancer AD 1.0 All P and LP
12+
HGNC:1101 ENSG00000139618 675 BRCA2 600185 Hereditary breast and ovarian cancer 612555 Cancer AD 1.0 All P and LP
13+
HGNC:1122 ENSG00000169814 686 BTD 609019 Biotinidase deficiency 253260 Metabolic AR 3.0 P and LP (2 variants)
14+
HGNC:1397 ENSG00000081248 779 CACNA1S 114208 Malignant hyperthermia 601887 Miscellaneous AD 1.0 All P and LP
15+
HGNC:1513 ENSG00000118729 845 CASQ2 114251 Catecholaminergic polymorphic ventricular tachycardia 611938 Cardiovascular AR 3.0 P and LP (2 variants)
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HGNC:2201 ENSG00000168542 1281 COL3A1 120180 Ehlers-Danlos syndrome, vascular type 130050 Cardiovascular AD 1.0 All P and LP
17+
HGNC:2770 ENSG00000175084 1674 DES 125660 Dliated cardiomyopathy 604765 Cardiovascular AD 3.1 All P and LP
18+
HGNC:2770 ENSG00000175084 1674 DES 125660 Myofibrillar myopathy 601419 Cardiovascular AD 3.1 All P and LP
19+
HGNC:3036 ENSG00000134755 1824 DSC2 125645 Arrhythmogenic right ventricular cardiomyopathy 610476 Cardiovascular AD 1.0 All P and LP
20+
HGNC:3049 ENSG00000046604 1829 DSG2 125671 Arrhythmogenic right ventricular cardiomyopathy 610193 Cardiovascular AD 1.0 All P and LP
21+
HGNC:3052 ENSG00000096696 1832 DSP 125647 Arrhythmogenic right ventricular cardiomyopathy 607450 Cardiovascular AD 1.0 All P and LP
22+
HGNC:3052 ENSG00000096696 1832 DSP 125647 Dilated cardiomyopathy 615821 Cardiovascular AD 1.0 All P and LP
23+
HGNC:3349 ENSG00000106991 2022 ENG 131195 Hereditary hemorrhagic telangiectasia 187300 Miscellaneous AD 3.0 All P and LP
24+
HGNC:3603 ENSG00000166147 2200 FBN1 134797 Marfan syndrome 154700 Cardiovascular AD 1.0 All P and LP
25+
HGNC:3756 ENSG00000128591 2318 FLNC 102565 Dilated cardiomyopathy 617047 Cardiovascular AD 3.0 All P and LP
26+
HGNC:3756 ENSG00000128591 2318 FLNC 102565 Myofibrillar myopathy 609524 Cardiovascular AD 3.0 All P and LP
27+
HGNC:4065 ENSG00000171298 2548 GAA 606800 Pompe disease 232300 Metabolic AR 3.0 P and LP (2 variants)
28+
HGNC:4296 ENSG00000102393 2717 GLA 300644 Fabry disease 301500 Cardiovascular Metabolic XL 1.0 All hemi, het, homozygous P and LP
29+
HGNC:4886 ENSG00000010704 3077 HFE 613609 Hereditary hemochromatosis (c.845G>A; p.C282Y homozygotes only) 235200 Miscellaneous AR 3.0 p.C282Y homozygotes only
30+
HGNC:11621 ENSG00000135100 6927 HNF1A 142410 Maturity-Onset of Diabetes of the Young 600496 Miscellaneous AD 3.0 All P and LP
31+
HGNC:6251 ENSG00000055118 3757 KCNH2 152427 Long-QT syndrome type 2 613688 Cardiovascular AD 1.0 All P and LP
32+
HGNC:6294 ENSG00000053918 3784 KCNQ1 607542 Long-QT syndrome type 1 192500 Cardiovascular AD 1.0 All P and LP
33+
HGNC:6547 ENSG00000130164 3949 LDLR 606945 Familial hypercholesterolemia 143890 Cardiovascular AD 1.0 All P and LP
34+
HGNC:6636 ENSG00000160789 4000 LMNA 150330 Dilated cardiomyopathy 115200 Cardiovascular AD 1.0 All P and LP
35+
HGNC:6913 ENSG00000125952 4149 MAX 154950 Hereditary paraganglioma-pheochromocytoma syndrome 171300 Cancer AD 3.0 All P and LP
36+
HGNC:7010 ENSG00000133895 4221 MEN1 613733 Multiple endocrine neoplasia type 1 131100 Cancer AD 1.0 All P and LP
37+
HGNC:7127 ENSG00000076242 4292 MLH1 120436 Lynch syndrome 609310 Cancer AD 1.0 All P and LP
38+
HGNC:7325 ENSG00000095002 4436 MSH2 609309 Lynch syndrome 120435 Cancer AD 1.0 All P and LP
39+
HGNC:7329 ENSG00000116062 2956 MSH6 600678 Lynch syndrome 614350 Cancer AD 1.0 All P and LP
40+
HGNC:7527 ENSG00000132781 4595 MUTYH 604933 MUTYH-associated polyposis 608456 Cancer AR 1.0 P and LP (2 variants)
41+
HGNC:7551 ENSG00000134571 4607 MYBPC3 600958 Hypertrophic cardiomyopathy 115197 Cardiovascular AD 1.0 All P and LP
42+
HGNC:7569 ENSG00000133392 4629 MYH11 160745 Familial thoracic aortic aneurysm 132900 Cardiovascular AD 1.0 All P and LP
43+
HGNC:7577 ENSG00000092054 4625 MYH7 160760 Hypertrophic cardiomyopathy 192600 Cardiovascular AD 1.0 All P and LP
44+
HGNC:7577 ENSG00000092054 4625 MYH7 160760 Dilated cardiomyopathy 613426 Cardiovascular AD 1.0 All P and LP
45+
HGNC:7583 ENSG00000111245 4633 MYL2 160781 Hypertrophic cardiomyopathy 608758 Cardiovascular AD 1.0 All P and LP
46+
HGNC:7584 ENSG00000160808 4634 MYL3 160790 Hypertrophic cardiomyopathy 608751 Cardiovascular AD 1.0 All P and LP
47+
HGNC:7773 ENSG00000186575 4771 NF2 607379 Neurofibromatosis type 2 101000 Cancer AD 1.0 All P and LP
48+
HGNC:8512 ENSG00000036473 5009 OTC 300461 Ornithine transcarbamylase deficiency 311250 Metabolic XL 2.0 All hemi, het, homozygous P and LP
49+
HGNC:26144 ENSG00000083093 79728 PALB2 610355 Hereditary breast cancer 114480 Cancer AD 3.0 All P and LP
50+
HGNC:20001 ENSG00000169174 255738 PCSK9 607786 Familial hypercholesterolemia 603776 Cardiovascular AD 1.0 All P and LP
51+
HGNC:9024 ENSG00000057294 5318 PKP2 602861 Arrhythmogenic right ventricular cardiomyopathy 609040 Cardiovascular AD 1.0 All P and LP
52+
HGNC:9122 ENSG00000122512 5395 PMS2 600259 Lynch syndrome 614337 Cancer AD 1.0 All P and LP
53+
HGNC:9386 ENSG00000106617 51422 PRKAG2 602743 Hypertrophic cardiomyopathy 600858 Cardiovascular Metabolic AD 1.0 All P and LP
54+
HGNC:9588 ENSG00000171862 5728 PTEN 601728 PTEN hamartoma tumor syndrome 158350 Cancer AD 1.0 All P and LP
55+
HGNC:9884 ENSG00000139687 5925 RB1 614041 Retinoblastoma 180200 Cancer AD 1.0 All P and LP
56+
HGNC:27424 ENSG00000203867 282996 RBM20 613171 Dliated cardiomyopathy 613172 Cardiovascular AD 3.1 All P and LP
57+
HGNC:9967 ENSG00000165731 5979 RET 164761 Familial medullary thyroid cancer 155240 Cancer AD 1.0 All P and LP
58+
HGNC:9967 ENSG00000165731 5979 RET 164761 Multiple endocrine neoplasia type 2A 171400 Cancer AD 1.0 All P and LP
59+
HGNC:9967 ENSG00000165731 5979 RET 164761 Multiple endocrine neoplasia type 2B 162300 Cancer AD 1.0 All P and LP
60+
HGNC:10294 ENSG00000116745 6121 RPE65 180069 RPE65-related retinopathy 204100, 613794 Miscellaneous AR 3.0 P and LP (2 variants)
61+
HGNC:10483 ENSG00000196218 6261 RYR1 180901 Malignant hyperthermia 145600 Miscellaneous AD 1.0 All P and LP
62+
HGNC:10484 ENSG00000198626 6262 RYR2 180902 Catecholaminergic polymorphic ventricular tachycardia 604772 Cardiovascular AD 1.0 All P and LP
63+
HGNC:10593 ENSG00000183873 6331 SCN5A 600163 Long QT syndrome type 3 603830 Cardiovascular AD 1.0 All P and LP
64+
HGNC:10593 ENSG00000183873 6331 SCN5A 600163 Brugada syndrome 601144 Cardiovascular AD 1.0 All P and LP
65+
HGNC:10593 ENSG00000183873 6331 SCN5A 600163 Dilated cardiomyopathy 601154 Cardiovascular AD 1.0 All P and LP
66+
HGNC:26034 ENSG00000167985 54949 SDHAF2 613019 Hereditary paraganglioma-pheochromocytoma syndrome 601650 Cancer AD 1.0 All P and LP
67+
HGNC:10681 ENSG00000117118 6390 SDHB 185470 Hereditary paraganglioma-pheochromocytoma syndrome 115310, 171300 Cancer AD 1.0 All P and LP
68+
HGNC:10682 ENSG00000143252 6391 SDHC 602413 Hereditary paraganglioma-pheochromocytoma syndrome 605373 Cancer AD 1.0 All P and LP
69+
HGNC:10683 ENSG00000204370 6392 SDHD 602690 Hereditary paraganglioma-pheochromocytoma syndrome 168000, 171300 Cancer AD 1.0 All P and LP
70+
HGNC:6769 ENSG00000166949 4088 SMAD3 603109 Loeys-Dietz syndrome 613795 Cardiovascular AD 1.0 All P and LP
71+
HGNC:6770 ENSG00000141646 4089 SMAD4 600993 Juvenile polyposis syndrome 174900 Cancer AD 1.0 All P and LP
72+
HGNC:6770 ENSG00000141646 4089 SMAD4 600993 Hereditary hemorrhagic telangiectasia 175050 Miscellaneous AD 1.0 All P and LP
73+
HGNC:11389 ENSG00000118046 6794 STK11 602216 Peutz-Jeghers syndrome 175200 Cancer AD 1.0 All P and LP
74+
HGNC:11772 ENSG00000106799 7046 TGFBR1 190181 Loeys-Dietz syndrome 609192 Cardiovascular AD 1.0 All P and LP
75+
HGNC:11773 ENSG00000163513 7048 TGFBR2 190182 Loeys-Dietz syndrome 610168 Cardiovascular AD 1.0 All P and LP
76+
HGNC:26038 ENSG00000135956 55654 TMEM127 613403 Hereditary paraganglioma-pheochromocytoma syndrome 171300 Cancer AD 3.0 All P and LP
77+
HGNC:28472 ENSG00000170876 79188 TMEM43 612048 Arrhythmogenic right ventricular cardiomyopathy 604400 Cardiovascular AD 1.0 All P and LP
78+
HGNC:11943 ENSG00000114854 7134 TNNC1 191040 Dilated cardiomyopathy 611879 Cardiovascular AD 3.1 All P and LP
79+
HGNC:11947 ENSG00000129991 7137 TNNI3 191044 Hypertrophic cardiomyopathy 613690 Cardiovascular AD 1.0 All P and LP
80+
HGNC:11949 ENSG00000118194 7139 TNNT2 191045 Dilated cardiomyopathy 601494 Cardiovascular AD 1.0 All P and LP
81+
HGNC:11949 ENSG00000118194 7139 TNNT2 191045 Hypertrophic cardiomyopathy 115195 Cardiovascular AD 1.0 All P and LP
82+
HGNC:11998 ENSG00000141510 7157 TP53 191170 Li-Fraumeni syndrome 151623 Cancer AD 1.0 All P and LP
83+
HGNC:12010 ENSG00000140416 7168 TPM1 191010 Hypertrophic cardiomyopathy 115196 Cardiovascular AD 1.0 All P and LP
84+
HGNC:12261 ENSG00000186439 10345 TRDN 603283 Catecholaminergic polymorphic ventricular tachycardia 615441 Cardiovascular AR 3.0 All P and LP
85+
HGNC:12261 ENSG00000186439 10345 TRDN 603283 Long QT syndrome n/a Cardiovascular AR 3.0 All P and LP
86+
HGNC:12362 ENSG00000165699 7248 TSC1 605284 Tuberous sclerosis complex 191100 Cancer AD 1.0 All P and LP
87+
HGNC:12363 ENSG00000103197 7249 TSC2 191092 Tuberous sclerosis complex 613254 Cancer AD 1.0 All P and LP
88+
HGNC:12403 ENSG00000155657 7273 TTN 188840 Dilated cardiomyopathy (truncating variants only) 604145 Cardiovascular AD 3.0 P and LP (truncating variants only)
89+
HGNC:12405 ENSG00000118271 7276 TTR 176300 Hereditary transthyretin-related amyloidosis 105210 Miscellaneous AD 3.1 All P and LP
90+
HGNC:12687 ENSG00000134086 7428 VHL 608537 Von Hippel-Lindau syndrome 193300 Cancer AD 1.0 All P and LP
91+
HGNC:12796 ENSG00000184937 7490 WT1 607102 WT1-related Wilms tumor 194070 Cancer AD 1.0 All P and LP

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