### LOVD-version 3000-270 ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = PHGDH) # 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}}" "PHGDH" "phosphoglycerate dehydrogenase" "1" "p12" "unknown" "NG_009188.1" "UD_132118520185" "" "http://www.LOVD.nl/PHGDH" "" "1" "8923" "26227" "606879" "1" "1" "1" "1" "Establishment of this gene variant database (LSDB) was supported by the Leiden University Medical Center (LUMC), Leiden, Nederland." "" "g" "http://databases.lovd.nl/shared/refseq/PHGDH_codingDNA.html" "1" "" "" "-1" "" "-1" "00001" "2013-05-03 00:00:00" "00006" "2016-06-19 12:04:33" "03840" "2022-04-13 19:19:03" ## 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}}" "00016094" "PHGDH" "phosphoglycerate dehydrogenase" "001" "NM_006623.3" "" "NP_006614.2" "" "" "" "-227" "1788" "1602" "120254419" "120286849" "" "0000-00-00 00:00:00" "" "" ## Diseases ## Do not remove or alter this header ## ## Count = 5 "{{id}}" "{{symbol}}" "{{name}}" "{{inheritance}}" "{{id_omim}}" "{{tissues}}" "{{features}}" "{{remarks}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "00139" "ID" "intellectual disability (ID)" "" "" "" "" "" "00084" "2013-06-04 18:18:07" "00006" "2015-02-09 10:02:49" "00198" "?" "unclassified / mixed" "" "" "" "" "" "00006" "2013-09-13 14:21:47" "00006" "2016-10-22 17:54:40" "00401" "NLS1" "Neu-Laxova syndrome (NLS)" "AR" "256520" "" "" "" "00006" "2014-06-06 10:12:33" "00006" "2021-12-10 21:51:32" "02392" "PHGDHD" "deficiency, phosphoglycerate dehydrogenase (PHGDHD)" "AR" "601815" "" "" "" "00006" "2014-09-25 23:29:40" "00006" "2021-12-10 21:51:32" "04214" "retinal disease" "retinal disease" "" "" "" "" "" "00006" "2015-02-27 19:48:07" "00006" "2020-08-25 10:54:40" ## Genes_To_Diseases ## Do not remove or alter this header ## ## Count = 3 "{{geneid}}" "{{diseaseid}}" "PHGDH" "00139" "PHGDH" "00401" "PHGDH" "02392" ## Individuals ## Do not remove or alter this header ## ## Count = 10 "{{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}}" "00016941" "" "" "" "2" "" "00705" "{PMID:Shaheen 2014:24836451}" "2-generation family, 2 affected/2 spontaneous abortions, unaffected heterozygous carrier parents, sister died immediately after birth" "F" "yes" "Saudi Arabia" "00y00m00d" "0" "" "" "Saudi" "" "00016942" "" "" "" "1" "" "00705" "{PMID:Shaheen 2014:24836451}" "2-generation family, 1 affected, unaffected heterozygous carrier parents" "?" "yes" "Saudi Arabia" "00y00m00d" "0" "" "" "Saudi" "" "00016943" "" "" "" "1" "" "00705" "{PMID:Shaheen 2014:24836451}" "2-generation family, 1 affected, unaffected parents" "M" "yes" "Saudi Arabia" "00y01m" "0" "" "" "Saudi" "" "00180172" "" "" "" "1" "" "00006" "{PMID:Tumienė 2018:29286531}" "" "" "" "(Slovenia)" "" "0" "" "" "" "29286531-Pat24" "00289502" "" "" "" "1" "" "03575" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "analysis 2794 individuals (India)" "" "" "India" "" "0" "" "" "" "" "00295965" "" "" "" "1" "" "02264" "" "" "F" "no" "Australia" "00y01m01d00h" "0" "" "" "" "3" "00295966" "" "" "" "1" "" "02264" "" "" "M" "yes" "Iran" "" "0" "" "" "" "" "00299923" "" "" "" "1" "" "02264" "" "" "F" "no" "France" "00y00m00d00h" "" "" "" "white" "" "00300227" "" "" "" "1" "" "02264" "" "" "F" "?" "Canada" "00y00m00d23h" "" "" "" "pakistan" "" "00408103" "" "" "" "1" "" "00000" "{PMID:Alabdullatif 2017:27717089}" "" "M" "yes" "United Arab Emirates" "" "0" "" "" "" "209" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 10 "{{individualid}}" "{{diseaseid}}" "00016941" "00401" "00016942" "00401" "00016943" "00401" "00180172" "00198" "00289502" "00198" "00295965" "00401" "00295966" "00401" "00299923" "00401" "00300227" "00401" "00408103" "04214" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 00139, 00198, 00401, 02392, 04214 ## Count = 11 "{{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}}" "0000015307" "00401" "00016941" "00705" "Familial, autosomal recessive" "00y00m00d" "born vaginally, died immediately after birth, very small for gestational age and had severe microcephaly (records of actual growth parameters at birth could not be retrieved), micrognathia, bulging eyes with absent\r\neyelids, severe ichthyosis of the skin, cleft lip and palate on the right side, a very flat nose, a very short neck, and generalized edema. Also had extremely abnormal limbs with hypoplastic forearms and no discernible digits in the upper or lower limbs." "" "" "" "" "" "" "" "" "" "" "" "0000015308" "00401" "00016942" "00705" "Familial, autosomal recessive" "00y00m00d" "born preterm 29w after an uneventful vaginal\r\ndelivery. Antenatal ultrasounds at both 19 and 24w of gestation showed polyhydramnios, curved vertebrae,\r\nprotruded eyes, an open mouth, low-set ears, a short and broad neck, microcephaly, generalized skin edema (especially of the trunk and scalp), abnormally flexed hands,\r\nextended crossed feet with a rocker-bottom appearance, and fetal akinesia. Postnatal screening for congenital infection was inconclusive. Postnatal examination revealed\r\nmassive body swelling and marked disfigurement of the\r\nface and limbs, which appeared engulfed by a thin and\r\nshiny membrane (Figure S1B). The eyes were small, fixed,\r\nand widely spaced and showed supraorbital massive cystic\r\nswelling bilaterally. The nose was completely flat and obliterated,\r\nand the mouth was large and fixed open with\r\nmassively swollen lips. The neck was extremely short.\r\nThe ear lobules were edematous with tight overlying\r\nskin. The trunk was short and shiny with visible veins.\r\nThe baby exhibited a fixed-flexion appearance with generalized\r\ncontractures. The massively edematous hands and\r\nfeet had no discernible digits. A skeletal survey showed\r\ndefaced and overlapping cranial bones with severe softtissue\r\nedema. Thoracic, vertebral, pelvic, and other tubular\r\nbones had no major skeletal defects" "" "" "" "" "" "" "" "" "" "" "" "0000015309" "00401" "00016943" "00705" "Familial, autosomal recessive" "00y" "delivered vaginally at term with thick meconium-stained liquor. Birth weight was 2.24 kg. The baby was evidently jaundiced with generalized colloidonlike ichthyosis. He was microcephalic (head circumferenceof 27.5 cm) with a sloping forehead, a broad nose, large ears, a short neck, spastic long fingers, and fixed contractures of the extremities. He succumbed to pneumonia and pseudomonas sepsis and died at 1 month of age." "" "" "" "" "" "" "" "" "" "" "" "0000142626" "00198" "00180172" "00006" "Familial, X-linked recessive" "" "(Pharmacoresistant severe) epileptic encephalopathy (HP:0200134), cerebral palsy (HP:0100021), profound global developmental delay (HP:0012736), microcephaly (HP:0000252). Head MRI: cerebral atrophy (HP:0002283)." "" "" "" "" "" "" "" "" "PDHAD, no lactic acidosis" "epilepsy or seizures associated with neurodevelopmental disorders and/or congenital malformations" "" "0000142649" "00198" "00180172" "00006" "Familial, autosomal recessive" "" "(Pharmacoresistant severe) epileptic encephalopathy (HP:0200134), cerebral palsy (HP:0100021), profound global developmental delay (HP:0012736), microcephaly (HP:0000252). Head MRI: cerebral atrophy (HP:0002283)." "" "" "" "" "" "" "" "" "PHGDHD" "epilepsy or seizures associated with neurodevelopmental disorders and/or congenital malformations" "" "0000227010" "00401" "00295965" "02264" "Familial, autosomal recessive" "" "HP:0000340, HP:0000470, HP:0000369, HP:0000347, HP:0001511, HP:0000252, HP:0001838, HP:0008064" "" "" "" "" "" "" "" "" "" "" "" "0000227011" "00401" "00295966" "02264" "Familial, autosomal recessive" "" "HP:0001511, HP:0000340, HP:0000470, HP:0000377, HP:0012472, HP:0000347, HP:0000520, HP:0000252, HP:0001339, HP:0001321, HP:0006101, HP:0001838, HP:0002650, HP:0008064, HP:0002089, HP:0001770, HP:0003241" "" "" "" "" "" "" "" "" "" "" "" "0000227013" "00401" "00295966" "02264" "Familial, autosomal recessive" "" "HP:0001371" "" "" "" "" "" "" "" "" "" "" "" "0000227245" "00401" "00299923" "02264" "Familial, autosomal recessive" "" "HP:0001511, HP:0000340, HP:0000470, HP:0000377, HP:0000369, HP:0000153, HP:0012472, HP:0000218, HP:0000347,HP:0003196, HP:0000463, HP:0007651,HP:0000518, HP:0000252, HP:0001339, HP:0001321, HP:00012714, HP:0000238, HP:0002514, HP:0001371, HP:0001762, HP:0005684, HP:0010557,HP:0008064,HP:0003241" "" "" "" "" "" "" "" "" "" "" "" "0000227528" "00401" "00300227" "02264" "Familial, autosomal recessive" "" "HP:0002126, HP:0001562, HP:0001558, HP:0001511, HP:0000340, HP:0000470, HP:0000377, HP:0000369, HP:0000153, HP:0000347, HP:0000316, HP: 0000445, HP:0008551, HP:0000520, HP:0000518, HP:0000252, HP:0001339, HP:0001321, HP:00012714, HP:0002119, HP:0001371, HP:0001838, HP:0000954, HP:0008064, HP:0000951, HP:0001196, HP:0002514, HP:0002089, HP:0003241" "" "" "" "" "" "" "" "" "" "" "" "0000300231" "04214" "00408103" "00000" "Familial, autosomal recessive" "6m" "6 months old male infant was born with prenatal course complicated by IUGR. At birth he was found to have microcephaly and generalized ichthyosis. At age of 3 weeks he was hospitalized due to decrease activity and poor feeding and found to have anemia that required blood transfusion. He also hand development delay, spasticity, microcephaly, short stature, failure to thrive, and distinctive facial features (hypertelorism, depressed nasal bridge, micrognathia, long smooth philtrum). Brain MRI showed brain atrophy and hypomyelination. Serine and glycine were low in plasma and CSF. Parents were from the same area and he had 4 healthy siblings." "" "" "" "" "" "" "" "" "Phosphoglycerate dehydrogenase deficiency" "" "" ## Screenings ## Do not remove or alter this header ## ## Count = 10 "{{id}}" "{{individualid}}" "{{variants_found}}" "{{owned_by}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "{{Screening/Technique}}" "{{Screening/Template}}" "{{Screening/Tissue}}" "{{Screening/Remarks}}" "0000016915" "00016941" "1" "00705" "00705" "2014-06-08 15:08:06" "" "" "SEQ" "DNA" "" "" "0000016916" "00016942" "1" "00705" "00705" "2014-06-08 15:27:45" "" "" "SEQ" "DNA" "" "" "0000016917" "00016943" "1" "00705" "00705" "2014-06-08 15:45:02" "" "" "SEQ" "DNA" "" "" "0000181075" "00180172" "1" "00006" "00006" "2018-08-24 19:40:22" "" "" "SEQ-NG" "DNA" "" "WES" "0000290670" "00289502" "1" "03575" "00006" "2020-03-11 19:30:02" "" "" "arraySNP" "DNA" "" "Infinium Global Screening Array v1.0" "0000297136" "00295965" "1" "02264" "02264" "2020-03-31 10:18:09" "" "" "SEQ;SEQ-NG" "DNA" "" "" "0000297137" "00295966" "1" "02264" "02264" "2020-03-31 10:47:06" "" "" "SEQ;SEQ-NG" "DNA" "" "" "0000301042" "00299923" "1" "02264" "02264" "2020-04-22 09:27:27" "" "" "SEQ" "DNA" "" "" "0000301342" "00300227" "1" "02264" "02264" "2020-04-24 10:49:33" "" "" "SEQ" "DNA" "" "" "0000409358" "00408103" "1" "00000" "03840" "2022-04-13 19:19:00" "" "" "arraySNP;SEQ" "DNA" "" "" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 9 "{{screeningid}}" "{{geneid}}" "0000016915" "PHGDH" "0000016916" "PHGDH" "0000016917" "PHGDH" "0000181075" "PDHA1" "0000297136" "PHGDH" "0000297137" "PHGDH" "0000301042" "PHGDH" "0000301342" "PHGDH" "0000409358" "PHGDH" ## 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 = 36 "{{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}}" "0000036872" "3" "70" "1" "120269633" "120269633" "subst" "0.00000406085" "00705" "PHGDH_000001" "g.120269633G>A" "" "{PMID:Shaheen 2014:24836451}" "" "" "" "Germline" "yes" "" "0" "" "" "g.119727010G>A" "" "likely pathogenic" "" "0000036873" "3" "70" "1" "120269633" "120269633" "subst" "0.00000406085" "00705" "PHGDH_000001" "g.120269633G>A" "" "{PMID:Shaheen 2014:24836451}" "" "" "" "Germline" "yes" "" "0" "" "" "g.119727010G>A" "" "likely pathogenic" "" "0000036874" "3" "70" "1" "120269703" "120269703" "subst" "0.00000406108" "00705" "PHGDH_000002" "g.120269703G>A" "" "{PMID:Shaheen 2014:24836451}" "" "" "" "Germline" "yes" "" "0" "" "" "g.119727080G>A" "" "likely pathogenic" "" "0000296940" "0" "10" "1" "120285546" "120285546" "subst" "0.690127" "02325" "PHGDH_000010" "g.120285546G>A" "" "" "" "PHGDH(NM_006623.4):c.1326G>A (p.T442=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.119742923G>A" "" "benign" "" "0000300739" "0" "10" "1" "120254545" "120254545" "subst" "0" "02326" "PHGDH_000003" "g.120254545G>C" "" "" "" "PHGDH(NM_006623.4):c.-101G>C" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.119711922G>C" "" "benign" "" "0000300740" "0" "90" "1" "120284428" "120284428" "subst" "0.0000081213" "02326" "PHGDH_000008" "g.120284428G>A" "" "" "" "PHGDH(NM_006623.4):c.1117G>A (p.A373T)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.119741805G>A" "" "pathogenic" "" "0000300741" "0" "90" "1" "120284440" "120284440" "subst" "0.0000121819" "02326" "PHGDH_000009" "g.120284440G>A" "" "" "" "PHGDH(NM_006623.4):c.1129G>A (p.G377S)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.119741817G>A" "" "pathogenic" "" "0000300742" "0" "10" "1" "120285546" "120285546" "subst" "0.690127" "02326" "PHGDH_000010" "g.120285546G>A" "" "" "" "PHGDH(NM_006623.4):c.1326G>A (p.T442=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.119742923G>A" "" "benign" "" "0000300743" "0" "70" "1" "120277980" "120277980" "subst" "0.0000529174" "02326" "PHGDH_000005" "g.120277980C>T" "" "" "" "PHGDH(NM_006623.4):c.706C>T (p.R236C)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.119735357C>T" "" "likely pathogenic" "" "0000300744" "0" "30" "1" "120279742" "120279742" "subst" "0" "02326" "PHGDH_000007" "g.120279742G>T" "" "" "" "PHGDH(NM_006623.4):c.798G>T (p.P266=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.119737119G>T" "" "likely benign" "" "0000305539" "0" "10" "1" "120277370" "120277370" "subst" "0.00145802" "01943" "PHGDH_000004" "g.120277370T>C" "" "" "" "PHGDH(NM_006623.3):c.624T>C (p.P208=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.119734747T>C" "" "benign" "" "0000320920" "0" "30" "1" "120278072" "120278072" "subst" "0.0110947" "01804" "PHGDH_000006" "g.120278072T>G" "" "" "" "PHGDH(NM_006623.3):c.792+6T>G (p.(=))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.119735449T>G" "" "likely benign" "" "0000404735" "1" "70" "1" "120263946" "120263946" "subst" "0.00000406699" "00006" "PHGDH_000012" "g.120263946T>C" "" "{PMID:Tumienė 2018:29286531}" "" "" "" "Germline" "" "" "0" "" "" "g.119721323T>C" "" "likely pathogenic" "ACMG" "0000404741" "2" "70" "1" "120269491" "120269491" "subst" "0.0000162427" "00006" "PHGDH_000013" "g.120269491C>T" "" "{PMID:Tumienė 2018:29286531}" "" "" "" "Germline" "" "" "0" "" "" "g.119726868C>T" "" "likely pathogenic" "ACMG" "0000502713" "0" "10" "1" "120254506" "120254506" "subst" "0" "02326" "PHGDH_000014" "g.120254506A>G" "" "" "" "PHGDH(NM_006623.4):c.-140A>G" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.119711883A>G" "" "benign" "" "0000502723" "0" "10" "1" "120277341" "120277341" "subst" "0.00140096" "01943" "PHGDH_000015" "g.120277341C>G" "" "" "" "PHGDH(NM_006623.3):c.595C>G (p.L199V)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.119734718C>G" "" "benign" "" "0000502724" "0" "50" "1" "120278072" "120278072" "subst" "0" "02326" "PHGDH_000016" "g.120278072T>C" "" "" "" "PHGDH(NM_006623.4):c.792+6T>C" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.119735449T>C" "" "VUS" "" "0000502725" "0" "30" "1" "120284469" "120284469" "subst" "0.000592874" "02326" "PHGDH_000017" "g.120284469G>T" "" "" "" "PHGDH(NM_006623.4):c.1158G>T (p.A386=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.119741846G>T" "" "likely benign" "" "0000502726" "0" "30" "1" "120286620" "120286620" "subst" "0.00108445" "02326" "PHGDH_000011" "g.120286620C>A" "" "" "" "PHGDH(NM_006623.4):c.1559C>A (p.A520E)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.119743997C>A" "" "likely benign" "" "0000604717" "0" "50" "1" "120277384" "120277384" "subst" "0.00000812407" "01804" "PHGDH_000018" "g.120277384C>T" "" "" "" "PHGDH(NM_006623.3):c.638C>T (p.(Thr213Met))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.119734761C>T" "" "VUS" "" "0000647359" "1" "50" "1" "120269520" "120269520" "subst" "0.0000121822" "03575" "PHGDH_000019" "g.120269520C>T" "1/2795 individuals" "{PMID:Narang 2020:32906206}, {DOI:Narang 2020:10.1002/humu.24102}" "" "" "1 heterozygous, no homozygous; {DB:CLININrs267606949}" "Germline" "" "rs267606949" "0" "" "" "g.119726897C>T" "" "VUS" "" "0000659758" "3" "70" "1" "120277384" "120277384" "subst" "0.00000812407" "02264" "PHGDH_000018" "g.120277384C>T" "" "" "" "" "" "Germline" "" "" "0" "" "" "g.119734761C>T" "" "pathogenic (recessive)" "" "0000659759" "3" "70" "1" "120277978" "120277978" "subst" "0" "02264" "PHGDH_000020" "g.120277978C>T" "" "" "" "" "" "Germline" "" "" "0" "" "" "g.119735355C>T" "" "pathogenic (recessive)" "" "0000663937" "3" "90" "1" "120263814" "120263814" "subst" "0.0000162427" "02264" "PHGDH_000021" "g.120263814C>T" "" "" "" "" "" "Germline" "" "" "0" "" "" "g.119721191C>T" "" "pathogenic (recessive)" "" "0000664261" "3" "90" "1" "120269703" "120269703" "subst" "0.00000406108" "02264" "PHGDH_000002" "g.120269703G>A" "" "" "" "" "" "Germline" "" "" "0" "" "" "g.119727080G>A" "" "pathogenic (recessive)" "" "0000675436" "0" "30" "1" "120282990" "120282990" "subst" "0.0000528868" "02326" "PHGDH_000022" "g.120282990G>A" "" "" "" "PHGDH(NM_006623.4):c.946-19G>A" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000716725" "0" "70" "1" "120263925" "120263928" "del" "0" "01943" "PHGDH_000023" "g.120263925_120263928del" "" "" "" "PHGDH(NM_006623.3):c.271_274delAAGG (p.K91Afs*5)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely pathogenic" "" "0000716726" "0" "30" "1" "120265981" "120265981" "subst" "0.000710666" "02326" "PHGDH_000024" "g.120265981C>A" "" "" "" "PHGDH(NM_006623.4):c.291-18C>A" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000716727" "0" "30" "1" "120266004" "120266004" "subst" "0.00117355" "02326" "PHGDH_000025" "g.120266004C>G" "" "" "" "PHGDH(NM_006623.4):c.296C>G (p.P99R)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000716728" "0" "50" "1" "120278013" "120278013" "subst" "0.000032652" "02325" "PHGDH_000026" "g.120278013C>T" "" "" "" "PHGDH(NM_006623.4):c.739C>T (p.R247W)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000716729" "0" "70" "1" "120284480" "120284480" "subst" "0" "01804" "PHGDH_000027" "g.120284480T>A" "" "" "" "PHGDH(NM_006623.3):c.1169T>A (p.(Leu390*))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely pathogenic" "" "0000716730" "0" "50" "1" "120286532" "120286532" "subst" "0.000106275" "01943" "HMGCS2_000025" "g.120286532C>T" "" "" "" "PHGDH(NM_006623.3):c.1471C>T (p.R491W)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000798712" "0" "50" "1" "120263815" "120263815" "subst" "0.0000203041" "01943" "PHGDH_000028" "g.120263815G>A" "" "" "" "PHGDH(NM_006623.3):c.161G>A (p.R54H)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000798713" "0" "30" "1" "120277295" "120277295" "subst" "0.0000406085" "01943" "PHGDH_000029" "g.120277295G>A" "" "" "" "PHGDH(NM_006623.3):c.549G>A (p.S183=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000798714" "0" "30" "1" "120285558" "120285558" "subst" "0.0000325002" "01943" "PHGDH_000030" "g.120285558G>C" "" "" "" "PHGDH(NM_006623.3):c.1338G>C (p.Q446H)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000846512" "3" "70" "1" "120285506" "120285506" "subst" "0" "00000" "PHGDH_000031" "g.120285506G>T" "" "{PMID:Alabdullatif 2017:27717089}" "" "PHGDH c.1286G>T, (p.Gly429Val)" "homozygous" "Germline" "yes" "" "0" "" "" "g.119742883G>T" "" "likely 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 PHGDH ## Count = 36 "{{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}}" "0000036872" "00016094" "70" "418" "0" "418" "0" "c.418G>A" "r.(?)" "p.(Gly140Arg)" "5" "0000036873" "00016094" "70" "418" "0" "418" "0" "c.418G>A" "r.(?)" "p.(Gly140Arg)" "5" "0000036874" "00016094" "70" "488" "0" "488" "0" "c.488G>A" "r.(?)" "p.(Arg163Gln)" "5" "0000296940" "00016094" "10" "1326" "0" "1326" "0" "c.1326G>A" "r.(?)" "p.(Thr442=)" "" "0000300739" "00016094" "10" "-101" "0" "-101" "0" "c.-101G>C" "r.(?)" "p.(=)" "" "0000300740" "00016094" "90" "1117" "0" "1117" "0" "c.1117G>A" "r.(?)" "p.(Ala373Thr)" "" "0000300741" "00016094" "90" "1129" "0" "1129" "0" "c.1129G>A" "r.(?)" "p.(Gly377Ser)" "" "0000300742" "00016094" "10" "1326" "0" "1326" "0" "c.1326G>A" "r.(?)" "p.(Thr442=)" "" "0000300743" "00016094" "70" "706" "0" "706" "0" "c.706C>T" "r.(?)" "p.(Arg236Cys)" "" "0000300744" "00016094" "30" "798" "0" "798" "0" "c.798G>T" "r.(?)" "p.(Pro266=)" "" "0000305539" "00016094" "10" "624" "0" "624" "0" "c.624T>C" "r.(?)" "p.(Pro208=)" "" "0000320920" "00016094" "30" "792" "6" "792" "6" "c.792+6T>G" "r.(=)" "p.(=)" "" "0000404735" "00016094" "70" "290" "2" "290" "2" "c.290+2T>C" "r.spl" "p.?" "2i" "0000404741" "00016094" "70" "374" "0" "374" "0" "c.374C>T" "r.(?)" "p.(Thr125Met)" "4" "0000502713" "00016094" "10" "-140" "0" "-140" "0" "c.-140A>G" "r.(?)" "p.(=)" "" "0000502723" "00016094" "10" "595" "0" "595" "0" "c.595C>G" "r.(?)" "p.(Leu199Val)" "" "0000502724" "00016094" "50" "792" "6" "792" "6" "c.792+6T>C" "r.(=)" "p.(=)" "" "0000502725" "00016094" "30" "1158" "0" "1158" "0" "c.1158G>T" "r.(?)" "p.(Ala386=)" "" "0000502726" "00016094" "30" "1559" "0" "1559" "0" "c.1559C>A" "r.(?)" "p.(Ala520Glu)" "" "0000604717" "00016094" "50" "638" "0" "638" "0" "c.638C>T" "r.(?)" "p.(Thr213Met)" "" "0000647359" "00016094" "50" "403" "0" "403" "0" "c.403C>T" "r.(?)" "p.(Arg135Trp)" "" "0000659758" "00016094" "70" "638" "0" "638" "0" "c.638C>T" "r.(?)" "p.(Thr213Met)" "6" "0000659759" "00016094" "70" "704" "0" "704" "0" "c.704C>T" "r.(?)" "p.(Ala235Val)" "7" "0000663937" "00016094" "90" "160" "0" "160" "0" "c.160C>T" "r.(?)" "p.(Arg54Cys)" "2" "0000664261" "00016094" "90" "488" "0" "488" "0" "c.488G>A" "r.(?)" "p.(Arg163Gln)" "" "0000675436" "00016094" "30" "946" "-19" "946" "-19" "c.946-19G>A" "r.(=)" "p.(=)" "" "0000716725" "00016094" "70" "271" "0" "274" "0" "c.271_274del" "r.(?)" "p.(Lys91Alafs*5)" "" "0000716726" "00016094" "30" "291" "-18" "291" "-18" "c.291-18C>A" "r.(=)" "p.(=)" "" "0000716727" "00016094" "30" "296" "0" "296" "0" "c.296C>G" "r.(?)" "p.(Pro99Arg)" "" "0000716728" "00016094" "50" "739" "0" "739" "0" "c.739C>T" "r.(?)" "p.(Arg247Trp)" "" "0000716729" "00016094" "70" "1169" "0" "1169" "0" "c.1169T>A" "r.(?)" "p.(Leu390*)" "" "0000716730" "00016094" "50" "1471" "0" "1471" "0" "c.1471C>T" "r.(?)" "p.(Arg491Trp)" "" "0000798712" "00016094" "50" "161" "0" "161" "0" "c.161G>A" "r.(?)" "p.(Arg54His)" "" "0000798713" "00016094" "30" "549" "0" "549" "0" "c.549G>A" "r.(?)" "p.(Ser183=)" "" "0000798714" "00016094" "30" "1338" "0" "1338" "0" "c.1338G>C" "r.(?)" "p.(Gln446His)" "" "0000846512" "00016094" "70" "1286" "0" "1286" "0" "c.1286G>T" "r.(?)" "p.(Gly429Val)" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 11 "{{screeningid}}" "{{variantid}}" "0000016915" "0000036872" "0000016916" "0000036873" "0000016917" "0000036874" "0000181075" "0000404735" "0000181075" "0000404741" "0000290670" "0000647359" "0000297136" "0000659758" "0000297137" "0000659759" "0000301042" "0000663937" "0000301342" "0000664261" "0000409358" "0000846512"