### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ###
## Filter: (gene_public = PTPN4)
# 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}}"
"PTPN4"	"protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)"	"2"	"q14.2"	"unknown"	"NC_000002.11"	"UD_136022289858"	""	"https://www.LOVD.nl/PTPN4"	""	"1"	"9656"	"5775"	"176878"	"1"	"1"	"1"	"1"	"Establishment of this gene variant database (LSDB) was performed by Johan den Dunnen, supported by <a href=\'http://www.variome.org\' target=\'_blank\'>Global Variome</a>."	""	"g"	"https://databases.lovd.nl/shared/refseq/PTPN4_codingDNA.html"	"1"	""	""	"-1"	""	"-1"	"00001"	"2013-05-03 00:00:00"	"00006"	"2025-01-09 09:15:56"	"00000"	"2025-11-01 13:22:20"


## 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}}"
"00017140"	"PTPN4"	"protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)"	"001"	"NM_002830.3"	""	"NP_002821.1"	""	""	""	"-771"	"10610"	"2781"	"120517207"	"120742475"	""	"0000-00-00 00:00:00"	""	""


## Diseases ## Do not remove or alter this header ##
## Count = 3
"{{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"
"05162"	"DD"	"developmental delay (DD)"	""	""	""	""	""	"00006"	"2016-05-10 21:15:54"	"00006"	"2020-05-25 13:52:33"
"05611"	"NDD"	"neurodevelopmental disorder (NDD)"	""	""	""	""	""	"00006"	"2019-06-19 12:27:20"	"00006"	"2024-12-13 11:12:21"


## Genes_To_Diseases ## Do not remove or alter this header ##
## Count = 0


## Individuals ## Do not remove or alter this header ##
## Count = 12
"{{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}}"
"00170836"	""	""	""	"1"	""	"02373"	""	""	"M"	"no"	"Poland"	">05y"	"0"	""	""	""	"R_1547"
"00459436"	""	""	""	"1"	""	"03544"	""	""	"M"	"-"	"- (not applicable)"	""	""	""	""	"white"	""
"00459532"	""	""	""	"1"	""	"00006"	"{PMID:Chmielewska 2024:34527963}"	"2-generation family, 1 affected, unaffected heterozygous carrier parents"	"M"	""	"United States"	""	"0"	""	""	"Europe;African-American"	"Pat1"
"00459533"	""	""	""	"1"	""	"00006"	"{PMID:Chmielewska 2024:34527963}"	"2-generation family, 1 affected, unaffected heterozygous carrier parents"	"M"	""	""	""	"0"	""	""	"Europe"	"Pat2"
"00459534"	""	""	""	"1"	""	"00006"	"{PMID:Chmielewska 2024:34527963}"	"2-generation family, 1 affected, unaffected heterozygous carrier parents"	"M"	""	"United States"	""	"0"	""	""	"Europe;African-American"	"Pat3"
"00459535"	""	""	""	"1"	""	"00006"	"{PMID:Chmielewska 2024:34527963}"	"2-generation family, 1 affected, unaffected heterozygous carrier parents"	"M"	""	""	""	"0"	""	""	"Europe"	"Pat4"
"00459536"	""	""	""	"1"	""	"00006"	"{PMID:Chmielewska 2024:34527963}"	"2-generation family, 1 affected, unaffected heterozygous carrier parents"	"F"	""	""	""	"0"	""	""	"Asia"	"Pat5"
"00459537"	""	""	""	"1"	""	"00006"	"{PMID:Chmielewska 2024:34527963}"	"2-generation family, 1 affected, unaffected heterozygous carrier parents"	"M"	""	""	""	"0"	""	""	"Europe"	"Pat6"
"00459538"	""	""	""	"1"	""	"00006"	"Corona-Rivera et al. (not paper listed), {PMID:Chmielewska 2024:34527963}"	"2-generation family, 1 affected, mosaicism in mother"	"F"	""	"Mexico"	""	"0"	""	""	"Europe"	"patient;PatA"
"00459539"	""	""	""	"1"	""	"00006"	"{PMID:Szczałuba 2018:30238967}, {PMID:Chmielewska 2024:34527963}"	"2-generation family, 1 affected, unaffected heterozygous carrier parents"	"M"	""	"Poland"	""	"0"	""	""	""	"patient;PatB"
"00459540"	""	""	""	"2"	""	"00006"	"{PMID:Christodolou 2015:25424712}, {PMID:Chmielewska 2024:34527963}"	"2-generation family, affected monozygotic twin pair, unaffected heterozygous carrier parents"	"F"	""	"Australia"	""	"0"	""	""	""	"twinA;PatC"
"00459541"	""	""	"00459540"	"1"	""	"00006"	"{PMID:Christodolou 2015:25424712}, {PMID:Chmielewska 2024:34527963}"	"monozygotic twin sister"	"F"	""	"Australia"	""	"0"	""	""	""	"twinB;PatD"


## Individuals_To_Diseases ## Do not remove or alter this header ##
## Count = 12
"{{individualid}}"	"{{diseaseid}}"
"00170836"	"05162"
"00459436"	"00198"
"00459532"	"05611"
"00459533"	"05611"
"00459534"	"05611"
"00459535"	"05611"
"00459536"	"05611"
"00459537"	"05611"
"00459538"	"05611"
"00459539"	"05611"
"00459540"	"05611"
"00459541"	"05611"


## Phenotypes ## Do not remove or alter this header ##
## Note: Only showing Phenotype columns active for Diseases 00198, 05162, 05611
## Count = 12
"{{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}}"
"0000135698"	"05162"	"00170836"	"02373"	"Isolated (sporadic)"	"03y"	"HP:0002033; HP:0002019; HP:0000682; HP:0001263; HP:0000750; HP:0002360; HP:0000733; HP:0003212"	""	"04y"	"childhood"	""	""	""	""	""	"developmental delay, autistic features, hypotonia, increased IgE and dental problems"	"developmental delay, autistic features, hypotonia, increased IgE and dental problems"	""
"0000347512"	"00198"	"00459436"	"03544"	"Isolated (sporadic)"	""	"HP:0000218, HP:0000268, HP:0000504, HP:0000520, HP:0000863, HP:0000954, HP:0000969, HP:0000980, HP:0001249, HP:0001250, HP:0001854, HP:0004887, HP:0100021"	""	""	""	""	""	""	""	""	"PTPN4-related disorder"	"complex neurodevelopmental disorder"	""
"0000347609"	"05611"	"00459532"	"00006"	"Isolated (sporadic)"	"11y"	"see paper; ..., height >99th percentile, OFC >99th percentile; attention deficit hyperactivity disorder, autism; developmental delay, no speech; tight hamstrings; MRI normal non-contrast; no muskuloskeletal anomalies; no cardiac anomalies; skin Café-au-lait macules; tapering fingers; crouch gait"	""	""	""	""	""	""	""	""	""	"neurodevelopmental delay"	""
"0000347610"	"05611"	"00459533"	"00006"	"Isolated (sporadic)"	"23m"	"see paper; ..., height 2nd percentile, OFC 79th percentile; no behavioral problems; developmental delay; hypotonia, distal extremity tremor; EEG normal; MRI large perivascular space/neuroglial cyst; no muskuloskeletal anomalies; no cardiac anomalies; skin Café-au-lait macules; tapering fingers; wide distal phalanges; strawberry hemangioma; wide-based gait"	""	""	""	""	""	""	""	""	""	"neurodevelopmental delay"	""
"0000347611"	"05611"	"00459534"	"00006"	"Isolated (sporadic)"	"20m"	"see paper; ..., height below 1st percentile (Z-4.84), OFC >99th percentile; no behavioral problems; developmental delay; congenital torticollis; MRI mildly diminished cerebral white matter volume, prominence of the ventricles and supratentorial extra-axial spaces may reflect white matter loss and or impaired cerebrospinal fluid resorption; radial deficiency with oligodactyly talipes equinovarus and vertebral anomalies (thoracic region block vertebrae with rib fusions and lumbosacral hemivertebra; pulmonary valve stenosis, aortic valve insufficiency, large ventricular septal defect and aberrant right subclavian artery; normal skin; meets criteria for VACTERL association"	""	""	""	""	""	""	""	""	""	"neurodevelopmental delay"	""
"0000347612"	"05611"	"00459535"	"00006"	"Isolated (sporadic)"	"19y"	"see paper; ..., height 71st percentile, OFC 99th percentile; attention deficit hyperactivity disorder, autism; moderate intellectual disability; normal tone, motor delays; no seizures; MRI large cavum septum pellucidum, slight reduction in white matter around posterior horns, thin corpus callosum; joint laxity, pes planus; no cardiac anomalies; normal skin; tapering fingers; joint laxity;, motor unsteadiness; astigmatism; hyperacusis"	""	""	""	""	""	""	""	""	""	"neurodevelopmental delay"	""
"0000347613"	"05611"	"00459536"	"00006"	"Unknown"	"15y"	"see paper; ..., height 30th percentile, OFC 7th percentile; attention deficit hyperactivity disorder; borderline intellectual disability; tic disorder; EEG abortive generalized spike wave discharges; MRI normal non-contrast; butterfly vertebrae; no cardiac anomalies; normal skin; visual processing deficit"	""	""	""	""	""	""	""	""	""	"neurodevelopmental delay"	""
"0000347614"	"05611"	"00459537"	"00006"	"Isolated (sporadic)"	"17y"	"see paper; ..., height 2nd percentile, OFC 98th percentile; attention deficit hyperactivity disorder; mild intellectual disability; neurologic exam normal; EEG abnormal; MRI normal; no muskuloskeletal anomalies; no cardiac anomalies; normal skin"	""	""	""	""	""	""	""	""	""	"neurodevelopmental delay"	""
"0000347615"	"05611"	"00459538"	"00006"	"Familial, autosomal dominant"	"1d"	"see paper; ..., height <1st percentile, severe microcephaly; small forehead, prominent sagittal suture; increased tone in all extremities ; semilobar holoprosencephaly and microcephaly, small 3rd ventricle, formed but thin splenium of corpus callosum, partial thalamic fusion, complete basal ganglia fusion, dorsal interhemispheric fissural cyst; hypoplastic left heart syndrome; normal skin"	""	""	""	""	""	""	""	""	""	"neurodevelopmental delay"	""
"0000347616"	"05611"	"00459539"	"00006"	"Isolated (sporadic)"	"05y"	"see paper; ..., pregnancy complicated by maternal kidney stones, hyperemesis; birth-37w cesarean section, weight 3580g (75th), length 56cm (50th), OFC 34cm (25th-50th); no congenital anomalies, no dysmorphic features; feeding difficulties, constipation, frequent infections, slightly raised body temperature, allergy to cow\'s milk; intellectual disability; developmental delay, autistic features; hypotonia; increased immunoglobulin E; 13m-delayed teeth eruption; neurologic sensory; MRI normal non-contrast; no muskuloskeletal anomalies; no cardiac anomalies"	""	""	""	""	""	""	""	""	""	"neurodevelopmental delay"	""
"0000347617"	"05611"	"00459540"	"00006"	"Isolated (sporadic)"	"17y"	"see paper; ..., normal pregnancy, normaldelivery brith-36w, weight 2670 g (50th ), length was 44.5cm (10th-50th), OFC 33.5 cm (50th); quiet/ placid baby; poor feeders, slow to gain weight; 9m- floppy, no roll-over, no crawl; 12m-sit, 3y4m-walk, 5y-single words; stereotypic hand movements; intellectual disability; seizures; EEG spike and wave generalised paroxysmal discharges; no muskuloskeletal anomalies; no cardiac anomalies"	""	""	""	""	""	""	""	""	""	"Rett syndrome-like"	""
"0000347618"	"05611"	"00459541"	"00006"	"Isolated (sporadic)"	"17y"	"see paper; ..., normal pregnancy, normal delivery, birth-36w, weight 2575 gm(10th–50th), length 44.5cm (10th–50th), OFC 33 cm (10th–50th; quiet/placid baby; poor feeder, slow to gain weight; 9m-floppy, no roll-over, no crawl; 15m-sit, 4y4m-walk, 6y-single words, 9y-lost speech; stereotypic behaviors; intellectual disability; generalized seizures; no muskuloskeletal anomalies; no cardiac anomalies"	""	""	""	""	""	""	""	""	""	"Rett syndrome-like"	""


## Screenings ## Do not remove or alter this header ##
## Count = 12
"{{id}}"	"{{individualid}}"	"{{variants_found}}"	"{{owned_by}}"	"{{created_by}}"	"{{created_date}}"	"{{edited_by}}"	"{{edited_date}}"	"{{Screening/Technique}}"	"{{Screening/Template}}"	"{{Screening/Tissue}}"	"{{Screening/Remarks}}"
"0000171719"	"00170836"	"1"	"02373"	"02373"	"2018-07-24 12:56:36"	""	""	"SEQ-NG-I"	"DNA"	"whole blood"	"whole exome sequencing"
"0000461061"	"00459436"	"1"	"03544"	"03544"	"2024-12-31 10:33:38"	""	""	"SEQ-NG-I"	"DNA"	"peripheral blood"	"WES"
"0000461158"	"00459532"	"1"	"00006"	"00006"	"2025-01-09 09:19:33"	""	""	"SEQ;SEQ-NG"	"DNA"	""	"WES"
"0000461159"	"00459533"	"1"	"00006"	"00006"	"2025-01-09 09:19:33"	""	""	"SEQ;SEQ-NG"	"DNA"	""	"WES"
"0000461160"	"00459534"	"1"	"00006"	"00006"	"2025-01-09 09:19:33"	""	""	"SEQ;SEQ-NG"	"DNA"	""	"WES"
"0000461161"	"00459535"	"1"	"00006"	"00006"	"2025-01-09 09:19:33"	""	""	"SEQ;SEQ-NG"	"DNA"	""	"WES"
"0000461162"	"00459536"	"1"	"00006"	"00006"	"2025-01-09 09:19:33"	""	""	"SEQ;SEQ-NG"	"DNA"	""	"WES"
"0000461163"	"00459537"	"1"	"00006"	"00006"	"2025-01-09 09:19:33"	""	""	"SEQ;SEQ-NG"	"DNA"	""	"WES"
"0000461164"	"00459538"	"1"	"00006"	"00006"	"2025-01-09 09:19:33"	""	""	"SEQ;SEQ-NG"	"DNA"	""	"WES"
"0000461165"	"00459539"	"1"	"00006"	"00006"	"2025-01-09 09:19:33"	""	""	"SEQ;SEQ-NG"	"DNA"	""	"WES"
"0000461166"	"00459540"	"1"	"00006"	"00006"	"2025-01-09 09:19:33"	""	""	"arrayCGH"	"DNA"	""	""
"0000461167"	"00459541"	"1"	"00006"	"00006"	"2025-01-09 09:19:33"	""	""	"arrayCGH"	"DNA"	""	""


## Screenings_To_Genes ## Do not remove or alter this header ##
## Count = 1
"{{screeningid}}"	"{{geneid}}"
"0000171719"	"PTPN4"


## 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 = 18
"{{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}}"
"0000392016"	"0"	"90"	"2"	"120620188"	"120620188"	"subst"	"0"	"02373"	"PTPN4_000001"	"g.120620188T>C"	"0"	""	""	""	"post-zygotic variant; amplicon deep sequencing results: 1. whole blood DNA 28%, 19673/71040 (variant reads/total reads); 2. hair follicles DNA 9%, 2606/30226 (variant reads/total reads)"	"De novo"	""	""	"0"	""	""	"g.119862612T>C"	""	"pathogenic"	""
"0000857684"	"0"	"50"	"2"	"120702656"	"120702656"	"subst"	"0"	"01804"	"PTPN4_000002"	"g.120702656G>A"	""	""	""	"PTPN4(NM_002830.3):c.1356-1G>A (p.?)"	"VKGL data sharing initiative Nederland"	"CLASSIFICATION record"	""	""	""	""	""	""	""	"VUS"	""
"0000991578"	"0"	"50"	"2"	"120677793"	"120677793"	"subst"	"0"	"01804"	"PTPN4_000003"	"g.120677793C>T"	""	""	""	"PTPN4(NM_002830.3):c.977C>T (p.(Thr326Ile))"	"VKGL data sharing initiative Nederland"	"CLASSIFICATION record"	""	""	""	""	""	""	""	"VUS"	""
"0000991579"	"0"	"30"	"2"	"120690059"	"120690059"	"subst"	"0"	"01804"	"PTPN4_000004"	"g.120690059C>T"	""	""	""	"PTPN4(NM_002830.3):c.1130C>T (p.(Ser377Leu))"	"VKGL data sharing initiative Nederland"	"CLASSIFICATION record"	""	""	""	""	""	""	""	"likely benign"	""
"0001020152"	"0"	"70"	"2"	"120639383"	"120639383"	"del"	"0"	"03544"	"PTPN4_000005"	"g.120639383del"	""	"{PMID:Chmielewska 2021:34527963} de novo missense and truncating variants in the PTPN4 gene in individuals with neurodevelopmental disorders and congenital abnormalities\r\n{PMID:Williamson 2015:25424712} de novo intragenic PTPN4 deletion in twins with RTT-like phenotype"	""	""	"ClinVar contains 7 pathogenic/likely pathogenic truncating or missense variants in the PTPN4 gene; de novo variant c.392_396del (VUS based on the character of the PTPN4 gene as a candidate gene according to the ACMG/AMP criteria) was found in an individual with developmental delay, short stature, congenital heart defect, skeletal abnormalities. The mentioned variant c.392_396del is located nearby the reported variant c.390del. Both variants are truncating, and individuals share similar phenotypic features."	"Germline"	"?"	""	"0"	""	""	"g.119881807del"	""	"likely pathogenic"	"ACMG"
"0001020284"	"0"	"50"	"2"	"120658333"	"120658333"	"subst"	"0"	"00006"	"PTPN4_000010"	"g.120658333G>A"	""	"{PMID:Chmielewska 2024:34527963}"	""	""	""	"De novo"	""	""	"0"	""	""	"g.119900757G>A"	""	"VUS"	"ACMG"
"0001020285"	"0"	"50"	"2"	"120620164"	"120620164"	"subst"	"0"	"00006"	"PTPN4_000006"	"g.120620164T>G"	""	"{PMID:Chmielewska 2024:34527963}"	""	""	"CUL3 variant associated with autism"	"De novo"	""	""	"0"	""	""	"g.119862588T>G"	""	"VUS"	"ACMG"
"0001020286"	"0"	"50"	"2"	"120639386"	"120639389"	"del"	"0"	"00006"	"PTPN4_000009"	"g.120639386_120639389del"	""	"{PMID:Chmielewska 2024:34527963}"	""	""	""	"De novo"	""	""	"0"	""	""	"g.119881810_119881813del"	""	"VUS"	"ACMG"
"0001020287"	"0"	"50"	"2"	"120718420"	"120718420"	"subst"	"0"	"00006"	"PTPN4_000012"	"g.120718420T>C"	""	"{PMID:Chmielewska 2024:34527963}"	""	""	""	"De novo"	""	""	"0"	""	""	"g.119960844T>C"	""	"VUS"	"ACMG"
"0001020288"	"0"	"50"	"2"	"120723175"	"120723175"	"subst"	"4.06134E-6"	"00006"	"PTPN4_000013"	"g.120723175C>T"	""	"{PMID:Chmielewska 2024:34527963}"	""	""	""	"Germline/De novo (untested)"	""	"rs1259252500"	"0"	""	""	"g.119965599C>T"	""	"VUS"	"ACMG"
"0001020289"	"0"	"50"	"2"	"120709630"	"120709630"	"subst"	"0"	"00006"	"PTPN4_000011"	"g.120709630G>T"	""	"{PMID:Corona-Rivera 2000:10706364}, {PMID:Chmielewska 2024:34527963}"	""	""	""	"De novo"	""	""	"0"	""	""	"g.119952054G>T"	""	"VUS"	"ACMG"
"0001020290"	"21"	"50"	"2"	"120723086"	"120723086"	"subst"	"0"	"00006"	"PTPN4_000007"	"g.120723086G>A"	""	"Corona-Rivera et al. (not paper listed), {PMID:Chmielewska 2024:34527963}"	""	""	"mosaic mother (9/96 reads); contributions STAG2 and PTPN4 variants to phenotype challenging to disentangle"	"Germline"	""	""	"0"	""	""	"g.119965510G>A"	""	"VUS"	"ACMG"
"0001020291"	"0"	"50"	"2"	"120620188"	"120620188"	"subst"	"0"	"00006"	"PTPN4_000001"	"g.120620188T>C"	""	"{PMID:Szczałuba 2018:30238967}, {PMID:Chmielewska 2024:34527963}"	""	""	"mosaic; variant PTPN4 did not localize to dendritic spines"	"De novo"	""	""	"0"	""	""	"g.119862612T>C"	""	"VUS"	"ACMG"
"0001020292"	"0"	"50"	"2"	"120584760"	"120726563"	"del"	"0"	"00006"	"PTPN4_000008"	"g.(120579294_120584760)_(120726563_120734950)del"	""	"{PMID:Christodolou 2015:25424712}, {PMID:Chmielewska 2024:34527963}"	""	"arr[hg19] 2q14.2(120,579,294-120,584,760)_(120,726,563-120,734,950)×1dn"	"90-160kb deletion affecting PTPN4"	"De novo"	""	""	"0"	""	""	"g.(119821718_119827184)_(119968987_119977374)del"	""	"VUS"	"ACMG"
"0001020293"	"0"	"50"	"2"	"120584760"	"120726563"	"del"	"0"	"00006"	"PTPN4_000008"	"g.(120579294_120584760)_(120726563_120734950)del"	""	"{PMID:Christodolou 2015:25424712}, {PMID:Chmielewska 2024:34527963}"	""	"arr[hg19] 2q14.2(120,579,294-120,584,760)_(120,726,563-120,734,950)×1dn"	"90-160kb deletion affecting PTPN4"	"De novo"	""	""	"0"	""	""	"g.(119821718_119827184)_(119968987_119977374)del"	""	"VUS"	"ACMG"
"0001050773"	"0"	"50"	"2"	"120635081"	"120635081"	"subst"	""	"01804"	"chr2_024161"	"g.120635081G>A"	""	""	""	"PTPN4(NM_002830.4):c.331G>A (p.(Val111Ile))"	"VKGL data sharing initiative Nederland"	"CLASSIFICATION record"	""	""	""	""	""	""	""	"VUS"	""
"0001050774"	"0"	"30"	"2"	"120672749"	"120672749"	"subst"	""	"01804"	"chr2_024162"	"g.120672749G>T"	""	""	""	"PTPN4(NM_002830.4):c.765-6G>T"	"VKGL data sharing initiative Nederland"	"CLASSIFICATION record"	""	""	""	""	""	""	""	"likely benign"	""
"0001050775"	"0"	"50"	"2"	"120718494"	"120718494"	"subst"	""	"01804"	"chr2_024163"	"g.120718494G>A"	""	""	""	"PTPN4(NM_002830.4):c.2245G>A (p.(Val749Ile))"	"VKGL data sharing initiative Nederland"	"CLASSIFICATION record"	""	""	""	""	""	""	""	"VUS"	""


## 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 PTPN4
## Count = 18
"{{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}}"
"0000392016"	"00017140"	"90"	"215"	"0"	"215"	"0"	"c.215T>C"	"r.(?)"	"p.(Leu72Ser)"	"3"
"0000857684"	"00017140"	"50"	"1356"	"-1"	"1356"	"-1"	"c.1356-1G>A"	"r.spl?"	"p.?"	""
"0000991578"	"00017140"	"50"	"977"	"0"	"977"	"0"	"c.977C>T"	"r.(?)"	"p.(Thr326Ile)"	""
"0000991579"	"00017140"	"30"	"1130"	"0"	"1130"	"0"	"c.1130C>T"	"r.(?)"	"p.(Ser377Leu)"	""
"0001020152"	"00017140"	"70"	"390"	"0"	"390"	"0"	"c.390del"	"r.(390del)"	"p.(Lys131Asnfs*19)"	"6"
"0001020284"	"00017140"	"50"	"715"	"0"	"715"	"0"	"c.715G>A"	"r.(?)"	"p.(Gly239Arg)"	""
"0001020285"	"00017140"	"50"	"191"	"0"	"191"	"0"	"c.191T>G"	"r.(?)"	"p.(Leu64Trp)"	""
"0001020286"	"00017140"	"50"	"393"	"0"	"396"	"0"	"c.393_396del"	"r.(?)"	"p.(Gln132ThrfsTer17)"	""
"0001020287"	"00017140"	"50"	"2171"	"0"	"2171"	"0"	"c.2171T>C"	"r.(?)"	"p.(Ile724Thr)"	""
"0001020288"	"00017140"	"50"	"2512"	"0"	"2512"	"0"	"c.2512C>T"	"r.(?)"	"p.(Arg838Ter)"	""
"0001020289"	"00017140"	"50"	"1738"	"0"	"1738"	"0"	"c.1738G>T"	"r.(?)"	"p.(Asp580Tyr)"	""
"0001020290"	"00017140"	"50"	"2423"	"0"	"2423"	"0"	"c.2423G>A"	"r.(?)"	"p.(Arg808His)"	""
"0001020291"	"00017140"	"50"	"215"	"0"	"215"	"0"	"c.215T>C"	"r.(?)"	"p.(Leu72Ser)"	""
"0001020292"	"00017140"	"50"	"138"	"17193"	"2694"	"1015"	"c.(138+11727_138+17193)_(2694+1015_*304)del"	"r.?"	"p.?"	"2i_27_"
"0001020293"	"00017140"	"50"	"138"	"17193"	"2694"	"1015"	"c.(138+11727_138+17193)_(2694+1015_*304)del"	"r.?"	"p.?"	"2i_27_"
"0001050773"	"00017140"	"50"	"331"	"0"	"331"	"0"	"c.331G>A"	"r.(?)"	"p.(Val111Ile)"	""
"0001050774"	"00017140"	"30"	"765"	"-6"	"765"	"-6"	"c.765-6G>T"	"r.(=)"	"p.(=)"	""
"0001050775"	"00017140"	"50"	"2245"	"0"	"2245"	"0"	"c.2245G>A"	"r.(?)"	"p.(Val749Ile)"	""


## Screenings_To_Variants ## Do not remove or alter this header ##
## Count = 12
"{{screeningid}}"	"{{variantid}}"
"0000171719"	"0000392016"
"0000461061"	"0001020152"
"0000461158"	"0001020284"
"0000461159"	"0001020285"
"0000461160"	"0001020286"
"0000461161"	"0001020287"
"0000461162"	"0001020288"
"0000461163"	"0001020289"
"0000461164"	"0001020290"
"0000461165"	"0001020291"
"0000461166"	"0001020292"
"0000461167"	"0001020293"