### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ###
## Filter: (gene_public = T)
# charset = UTF-8

## Genes ## Do not remove or alter this header ##
## Count = 1
"{{id}}"	"{{name}}"	"{{chromosome}}"	"{{chrom_band}}"	"{{imprinting}}"	"{{refseq_genomic}}"	"{{refseq_UD}}"	"{{reference}}"	"{{url_homepage}}"	"{{url_external}}"	"{{allow_download}}"	"{{id_hgnc}}"	"{{id_entrez}}"	"{{id_omim}}"	"{{show_hgmd}}"	"{{show_genecards}}"	"{{show_genetests}}"	"{{show_orphanet}}"	"{{note_index}}"	"{{note_listing}}"	"{{refseq}}"	"{{refseq_url}}"	"{{disclaimer}}"	"{{disclaimer_text}}"	"{{header}}"	"{{header_align}}"	"{{footer}}"	"{{footer_align}}"	"{{created_by}}"	"{{created_date}}"	"{{edited_by}}"	"{{edited_date}}"	"{{updated_by}}"	"{{updated_date}}"
"T"	"T, brachyury homolog (mouse)"	"6"	"q27"	"unknown"	"LRG_114"	"UD_134408276899"	""	"https://www.LOVD.nl/TBXT"	""	"1"	"11515"	"6862"	"601397"	"1"	"1"	"1"	"1"	"<font color=\"#FF0000\">NOTE: gene name changed from T to TBXT</font>\r\nEstablishment of this gene variant database (LSDB) was supported by the <a href=\'http://www.LUMC.nl\' target=\'_blank\'>Leiden University Medical Center (LUMC)</a>, Leiden, Nederland."	""	"g"	"https://databases.lovd.nl/shared/refseq/T_codingDNA.html"	"1"	""	"<font color=\"#FF0000\">NOTE: gene name changed from T to TBXT</font>"	"-1"	""	"-1"	"00001"	"2013-05-03 00:00:00"	"00006"	"2020-05-22 09:37:47"	"00000"	"2024-08-28 13:16:32"


## Transcripts ## Do not remove or alter this header ##
## Count = 1
"{{id}}"	"{{geneid}}"	"{{name}}"	"{{id_mutalyzer}}"	"{{id_ncbi}}"	"{{id_ensembl}}"	"{{id_protein_ncbi}}"	"{{id_protein_ensembl}}"	"{{id_protein_uniprot}}"	"{{remarks}}"	"{{position_c_mrna_start}}"	"{{position_c_mrna_end}}"	"{{position_c_cds_end}}"	"{{position_g_mrna_start}}"	"{{position_g_mrna_end}}"	"{{created_by}}"	"{{created_date}}"	"{{edited_by}}"	"{{edited_date}}"
"00020681"	"T"	"transcript variant 1"	"002"	"NM_003181.3"	""	"NP_003172.1"	""	""	""	"-519"	"1967"	"1308"	"166582157"	"166571144"	""	"0000-00-00 00:00:00"	""	""


## Diseases ## Do not remove or alter this header ##
## Count = 4
"{{id}}"	"{{symbol}}"	"{{name}}"	"{{inheritance}}"	"{{id_omim}}"	"{{tissues}}"	"{{features}}"	"{{remarks}}"	"{{created_by}}"	"{{created_date}}"	"{{edited_by}}"	"{{edited_date}}"
"00198"	"?"	"unclassified / mixed"	""	""	""	""	""	"00006"	"2013-09-13 14:21:47"	"00006"	"2024-11-23 09:38:12"
"00860"	"NTD"	"neural tube defects, susceptibility to (NTD)"	"AD"	"182940"	""	""	""	"00006"	"2014-09-25 23:29:40"	"00006"	"2021-12-10 21:51:32"
"04056"	"SAVA"	"sacral agenesis with vertebral anomalies"	"AR"	"615709"	""	""	""	"00006"	"2014-09-25 23:29:40"	"00006"	"2021-12-10 21:51:32"
"05342"	"CAKUT"	"kidney and urinary tract, anomalies, congenital (CAKUT)"	""	""	""	""	""	"00006"	"2017-11-10 19:49:59"	"00006"	"2017-11-10 19:51:20"


## Genes_To_Diseases ## Do not remove or alter this header ##
## Count = 2
"{{geneid}}"	"{{diseaseid}}"
"T"	"00860"
"T"	"04056"


## Individuals ## Do not remove or alter this header ##
## Count = 2
"{{id}}"	"{{fatherid}}"	"{{motherid}}"	"{{panelid}}"	"{{panel_size}}"	"{{license}}"	"{{owned_by}}"	"{{Individual/Reference}}"	"{{Individual/Remarks}}"	"{{Individual/Gender}}"	"{{Individual/Consanguinity}}"	"{{Individual/Origin/Geographic}}"	"{{Individual/Age_of_death}}"	"{{Individual/VIP}}"	"{{Individual/Data_av}}"	"{{Individual/Treatment}}"	"{{Individual/Origin/Population}}"	"{{Individual/Individual_ID}}"
"00132977"	""	""	""	"1"	""	"00006"	"{PMID:Sanna-Cherchi 2017:29100090}, {DOI:Sanna-Cherchi 2017:10.1016/j.ajhg.2017.09.018}"	""	"F"	""	""	""	"0"	""	""	""	"29100090-FamDC19"
"00301731"	""	""	""	"1"	""	"00006"	"{PMID:Maddirevula 2019:30237576}"	""	"F"	""	"Saudi Arabia"	""	"0"	""	""	""	"15DG1600"


## Individuals_To_Diseases ## Do not remove or alter this header ##
## Count = 2
"{{individualid}}"	"{{diseaseid}}"
"00132977"	"05342"
"00301731"	"00198"


## Phenotypes ## Do not remove or alter this header ##
## Note: Only showing Phenotype columns active for Diseases 00198, 00860, 04056, 05342
## Count = 2
"{{id}}"	"{{diseaseid}}"	"{{individualid}}"	"{{owned_by}}"	"{{Phenotype/Inheritance}}"	"{{Phenotype/Age}}"	"{{Phenotype/Additional}}"	"{{Phenotype/Age/Onset}}"	"{{Phenotype/Age/Diagnosis}}"	"{{Phenotype/Onset}}"	"{{Phenotype/Protein}}"	"{{Phenotype/Tumor/MSI}}"	"{{Phenotype/Enzyme/CPK}}"	"{{Phenotype/Heart/Myocardium}}"	"{{Phenotype/Lung}}"	"{{Phenotype/Diagnosis/Definite}}"	"{{Phenotype/Diagnosis/Initial}}"	"{{Phenotype/Diagnosis/Criteria}}"
"0000105738"	"05342"	"00132977"	"00006"	"Unknown"	""	"CAKUT, renal agenesis left"	""	""	""	""	""	""	""	""	""	""	""
"0000228829"	"00198"	"00301731"	"00006"	"Familial, autosomal recessive"	"2y10m"	"delivered normally at term. Mother was 26 years old G2P1+0. Antenatal U/S at 26 weeks gestation showed small head <5th centile, banana shaped cerebellum, and a mass at the lumbar spine. Examination showed no facial dysmorphic features. There was dorsolumbar myelomeningeocele (3x5 cm), leaking CSF, paraplegia with no movements in the lower limbs which were held in flexion at hips and extended knees, patulous anus with absent anal reflex. Sensations and reflexes were absent in the lower limbs. CT brain revealed hydrocephalus and Chiari malformation with prominent posterior fossa structures and herniated cerebellar vermis. MRI brain showed dilated lateral ventricles, the cerebellum is normally shaped, and it is low lying, with herniation of the vermis, and Arnold-Chiari malformation. The myelomeningocele was repaired, and she required ventriculoperitoneal shunt for subsequent hydrocephalus. She was incontinent of stools and urine. She developed urinary tract infections and sepsis with multidrug resistant klebsiella pneumonae. She was on ventilatory support, she also had refractory seizures. She died at the age of two years. Parents were first cousins and there was strong family history of neural tube defects. Her younger sister who also had neural tube defects and died at the age of 9 months with severe bronchiolitis causing respiratory failure."	""	""	""	""	""	""	""	""	""	""	""


## Screenings ## Do not remove or alter this header ##
## Count = 2
"{{id}}"	"{{individualid}}"	"{{variants_found}}"	"{{owned_by}}"	"{{created_by}}"	"{{created_date}}"	"{{edited_by}}"	"{{edited_date}}"	"{{Screening/Technique}}"	"{{Screening/Template}}"	"{{Screening/Tissue}}"	"{{Screening/Remarks}}"
"0000133811"	"00132977"	"1"	"00006"	"00006"	"2017-11-11 21:33:23"	""	""	"SEQ"	"DNA"	""	"WES"
"0000302855"	"00301731"	"1"	"00006"	"00006"	"2020-05-22 17:20:34"	""	""	"SEQ-NG"	"DNA"	""	"WES"


## Screenings_To_Genes ## Do not remove or alter this header ##
## Count = 2
"{{screeningid}}"	"{{geneid}}"
"0000133811"	"T"
"0000302855"	"T"


## Variants_On_Genome ## Do not remove or alter this header ##
## Please note that not necessarily all variants found in the given individuals are shown. This output is restricted to variants in the selected gene.
## Count = 7
"{{id}}"	"{{allele}}"	"{{effectid}}"	"{{chromosome}}"	"{{position_g_start}}"	"{{position_g_end}}"	"{{type}}"	"{{average_frequency}}"	"{{owned_by}}"	"{{VariantOnGenome/DBID}}"	"{{VariantOnGenome/DNA}}"	"{{VariantOnGenome/Frequency}}"	"{{VariantOnGenome/Reference}}"	"{{VariantOnGenome/Restriction_site}}"	"{{VariantOnGenome/Published_as}}"	"{{VariantOnGenome/Remarks}}"	"{{VariantOnGenome/Genetic_origin}}"	"{{VariantOnGenome/Segregation}}"	"{{VariantOnGenome/dbSNP}}"	"{{VariantOnGenome/VIP}}"	"{{VariantOnGenome/Methylation}}"	"{{VariantOnGenome/ISCN}}"	"{{VariantOnGenome/DNA/hg38}}"	"{{VariantOnGenome/ClinVar}}"	"{{VariantOnGenome/ClinicalClassification}}"	"{{VariantOnGenome/ClinicalClassification/Method}}"
"0000223239"	"0"	"70"	"6"	"166579302"	"166579302"	"subst"	"0"	"00006"	"T_000001"	"g.166579302T>G"	""	"{PMID:Sanna-Cherchi 2017:29100090}, {DOI:Sanna-Cherchi 2017:10.1016/j.ajhg.2017.09.018}"	""	""	"Variant Error [EREF/EREF]: This genomic variant does not match the reference sequence; the transcript variant does not match the reference sequence either. Please fix this entry and then remove this message."	"Germline"	""	""	"0"	""	""	"g.166165814T>G"	""	"likely pathogenic"	""
"0000655537"	"0"	"50"	"6"	"166580220"	"166580220"	"subst"	"1.22088E-5"	"01943"	"T_000002"	"g.166580220G>A"	""	""	""	"TBXT(NM_003181.3):c.331C>T (p.P111S)"	"VKGL data sharing initiative Nederland"	"CLASSIFICATION record"	""	""	""	""	""	"g.166166732G>A"	""	"VUS"	""
"0000666212"	"3"	"70"	"6"	"166580085"	"166580085"	"subst"	"0"	"00006"	"T_000003"	"g.166580085C>A"	""	"{PMID:Maddirevula 2019:30237576}"	""	""	"ACMG PVS2, PM2"	"Germline"	""	""	"0"	""	""	"g.166166597C>A"	""	"likely pathogenic (recessive)"	"ACMG"
"0000995548"	"0"	"50"	"6"	"166571990"	"166571990"	"subst"	"0"	"01804"	"T_000004"	"g.166571990T>C"	""	""	""	"T(NM_003181.3):c.1121A>G (p.(Gln374Arg))"	"VKGL data sharing initiative Nederland"	"CLASSIFICATION record"	""	""	""	""	""	""	""	"VUS"	""
"0000995549"	"0"	"30"	"6"	"166572065"	"166572065"	"subst"	"0"	"01804"	"T_000005"	"g.166572065C>T"	""	""	""	"T(NM_003181.3):c.1046G>A (p.(Ser349Asn))"	"VKGL data sharing initiative Nederland"	"CLASSIFICATION record"	""	""	""	""	""	""	""	"likely benign"	""
"0000995550"	"0"	"30"	"6"	"166574346"	"166574346"	"subst"	"0.00505215"	"01804"	"T_000006"	"g.166574346G>A"	""	""	""	"T(NM_003181.3):c.1013C>T (p.(Ala338Val))"	"VKGL data sharing initiative Nederland"	"CLASSIFICATION record"	""	""	""	""	""	""	""	"likely benign"	""
"0000995551"	"0"	"90"	"6"	"166579288"	"166579288"	"subst"	"0"	"01804"	"T_000007"	"g.166579288T>C"	""	""	""	"T(NM_003181.3):c.512A>G (p.(His171Arg))"	"VKGL data sharing initiative Nederland"	"CLASSIFICATION record"	""	""	""	""	""	""	""	"pathogenic"	""


## Variants_On_Transcripts ## Do not remove or alter this header ##
## Please note that not necessarily all variants found in the given individuals are shown. This output is restricted to variants in the selected gene.
## Note: Only showing Variants_On_Transcript columns active for Genes T
## Count = 7
"{{id}}"	"{{transcriptid}}"	"{{effectid}}"	"{{position_c_start}}"	"{{position_c_start_intron}}"	"{{position_c_end}}"	"{{position_c_end_intron}}"	"{{VariantOnTranscript/DNA}}"	"{{VariantOnTranscript/RNA}}"	"{{VariantOnTranscript/Protein}}"	"{{VariantOnTranscript/Exon}}"
"0000223239"	"00020681"	"70"	"498"	"0"	"498"	"0"	"c.498A>C"	"r.(?)"	"p.(TYr166*)"	""
"0000655537"	"00020681"	"50"	"331"	"0"	"331"	"0"	"c.331C>T"	"r.(?)"	"p.(Pro111Ser)"	""
"0000666212"	"00020681"	"70"	"466"	"0"	"466"	"0"	"c.466G>T"	"r.(?)"	"p.(Gly156Cys)"	""
"0000995548"	"00020681"	"50"	"1121"	"0"	"1121"	"0"	"c.1121A>G"	"r.(?)"	"p.(Gln374Arg)"	""
"0000995549"	"00020681"	"30"	"1046"	"0"	"1046"	"0"	"c.1046G>A"	"r.(?)"	"p.(Ser349Asn)"	""
"0000995550"	"00020681"	"30"	"1013"	"0"	"1013"	"0"	"c.1013C>T"	"r.(?)"	"p.(Ala338Val)"	""
"0000995551"	"00020681"	"90"	"512"	"0"	"512"	"0"	"c.512A>G"	"r.(?)"	"p.(His171Arg)"	""


## Screenings_To_Variants ## Do not remove or alter this header ##
## Count = 2
"{{screeningid}}"	"{{variantid}}"
"0000133811"	"0000223239"
"0000302855"	"0000666212"