### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = PGM2L1) # 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}}" "PGM2L1" "phosphoglucomutase 2-like 1" "11" "q13.3" "unknown" "NC_000011.9" "UD_132610802152" "" "https://www.LOVD.nl/PGM2L1" "" "1" "20898" "283209" "611610" "1" "1" "1" "1" "Establishment of this gene variant database (LSDB) was performed by Johan den Dunnen, supported by Global Variome." "" "g" "https://databases.lovd.nl/shared/refseq/PGM2L1_codingDNA.html" "1" "" "" "-1" "" "-1" "00000" "2012-09-13 00:00:00" "00006" "2023-02-08 19:38:14" "00006" "2023-02-08 20:47:54" ## 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}}" "00001200" "PGM2L1" "phosphoglucomutase 2-like 1" "001" "NM_173582.3" "" "NP_775853.2" "" "" "" "-296" "8205" "1869" "74041361" "74109502" "00000" "2012-09-13 13:18:37" "" "" ## 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}}" "01157" "CHTE" "Hypothyroidism, central, testicular enlargement (CHTE)" "XLR" "300888" "" "" "" "00006" "2014-09-25 23:29:40" "00006" "2021-12-10 21:51:32" "05611" "NDD" "neurodevelopmental disorder (NDD)" "" "" "" "" "" "00006" "2019-06-19 12:27:20" "00006" "2024-12-13 11:12:21" "07004" "NEDHFS" "neurodevelopmental disorder with hypotonia, dysmorphic facies, skin abnormalities" "AR" "620191" "" "" "" "00006" "2023-02-08 20:03:36" "" "" ## Genes_To_Diseases ## Do not remove or alter this header ## ## Count = 2 "{{geneid}}" "{{diseaseid}}" "PGM2L1" "05611" "PGM2L1" "07004" ## Individuals ## Do not remove or alter this header ## ## Count = 6 "{{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}}" "00000208" "" "" "" "1" "" "00037" "{PMID:Sun 2011:23143598}, {DOI:Sun 2011:10.1038/ng.2453}" "" "M" "no" "Netherlands" "" "0" "" "" "" "" "00000209" "" "" "" "1" "" "00037" "{PMID:Sun 2011:23143598}, {DOI:Sun 2011:10.1038/ng.2453}" "" "M" "no" "Netherlands" "" "0" "" "" "" "" "00431330" "" "" "" "1" "" "00006" "{PMID:Morova 2021:33979636}" "2-generation family, 1 affected, unaffected heterozygous carrier parents" "M" "" "Turkey" "" "0" "" "" "" "Pat1" "00431331" "" "" "" "1" "" "00006" "{PMID:Morova 2021:33979636}" "2-generation family, 1 affected, unaffected heterozygous carrier parents" "F" "" "Canada" "" "0" "" "" "French-Canadian (Cajun)" "Pat2" "00431332" "" "" "" "1" "" "00006" "{PMID:Morova 2021:33979636}" "2-generation family, 1 affected, unaffected heterozygous carrier parents" "F" "yes" "Denmark" "" "0" "" "" "Middle East" "Pat3(DECIPHER381996)" "00431333" "" "" "" "1" "" "00006" "{PMID:Morova 2021:33979636}" "2-generation family, 1 affected, unaffected heterozygous carrier parents" "F" "" "Pakistan" "" "0" "" "" "" "Pat4" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 6 "{{individualid}}" "{{diseaseid}}" "00000208" "01157" "00000209" "01157" "00431330" "05611" "00431331" "05611" "00431332" "05611" "00431333" "05611" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 01157, 05611, 07004 ## Count = 6 "{{id}}" "{{diseaseid}}" "{{individualid}}" "{{owned_by}}" "{{Phenotype/Inheritance}}" "{{Phenotype/Age}}" "{{Phenotype/Additional}}" "{{Phenotype/Age/Onset}}" "{{Phenotype/Age/Diagnosis}}" "{{Phenotype/Onset}}" "{{Phenotype/Protein}}" "{{Phenotype/Enzyme/CPK}}" "{{Phenotype/Heart/Myocardium}}" "{{Phenotype/Lung}}" "{{Phenotype/Diagnosis/Definite}}" "{{Phenotype/Diagnosis/Initial}}" "0000038983" "01157" "00000208" "00006" "Familial, X-linked recessive" "" "central hypothyroidism (FT4 0.50-0.99of lower limit normal), no prolactin deficiency, age sonographic determination testicular volume 17.64y, testicular volume right/left 21/20 (7.3–16ml)" "" "3w" "" "" "" "" "" "" "" "0000038984" "01157" "00000209" "00006" "Familial, X-linked recessive" "" "central hypothyroidism (FT4 0.50-0.99of lower limit normal), prolactin deficiency, age sonographic determination testicular volume 21.36y, testicular volume right/left 30/26 (8.5–18.3ml)" "" "07y04m" "" "" "" "" "" "" "" "0000321930" "05611" "00431330" "00006" "Familial, autosomal recessive" "7y" "see paper; ..., global development delay; intellectual disability; 18m-sit, 34m-walk; single words (4–5) at 34 months; no meaningful contact fter status epilepticus and resuscitation; neurologic features; hypotonia; muscle weakness; seizures; pyramidal signs after status epilepticus and resuscitation; no ataxia; MRI dilation frontal interhemispheric cleft; over-folded helices, large earlobes, pronounced antitragus; long eyelashes, down-slanting palpebral fissures; high arched narrow palate; flat nasal bridge, broad bulbous nasal tip, long philtrum; thin upper lip; pointy chin; early caries; skin abnormalities; dry skin, keratosis pilaris; hypertrichosis back; exotropia; no hypermetropia; vision loss after status epilepticus and resuscitation; gastro-intestinal abnormalities; swallowing difficulties after status epilepticus and resuscitation; early obesity; normal extremities; normal joints; normal hands/feet" "" "" "" "" "" "" "" "NEDHFS" "neurodevelopmental delay" "0000321931" "05611" "00431331" "00006" "Familial, autosomal recessive" "7y6m" "see paper; ..., global development delay; intellectual disability; 10m-sit, 18m-walk; severe speech delay; severe pica and aggressive behavior; neurologic features; truncal hypotonia; muscle weakness; seizures; no pyramidal signs; ataxia; MRI unremarkable (MRS showed decreased NAA and mildly elevated lactic acid); prominent ears, large ear lobes, and over-folded helices; epicanthal folds, down-slanting palpebral fissures; high arched narrow palate; prominent nasal tip, flat nasal bridge, under-developed nasolabial fold; thin upper lip; no pointy chin; early caries; skin abnormalities; dry skin, keratosis pilaris; excessive arm hair growth; exotropia; no hypermetropia; normal vision; no gastro-intestinal abnormalities; no swallowing difficulties; early obesity; normal hands/feet; hypermobility; small hands/feet, short toes" "" "" "" "" "" "" "" "NEDHFS" "neurodevelopmental delay" "0000321932" "05611" "00431332" "00006" "Familial, autosomal recessive" "7y" "see paper; ..., global development delay; intellectual disability; 7y-sit/stand with support, no targeted hand activity; severe, no verbal language; normal behavior; neurologic features; shifting tonus, with hypertonia; no muscle weakness; no seizures; no pyramidal signs; no ataxia; MRI symmetric infra/supra tentorial parenchymal anomalies, signal changes lower cerebellar hemispheres, nucleus lentiformis and scattered on the verge between cortex white matter; large earlobes; normal eyes; high arched narrow palate; prominent nose, flat philtrum; no thin upper lip; pointy chin; normal teeth; skin abnormalities; dry skin, keratosis pilaris; normal hair growth; exotropia; hypermetropia; normal vision; no gastro-intestinal abnormalities; no swallowing difficulties; no obesity; normal extremities; normal joints; normal hands/feet" "" "" "" "" "" "" "" "NEDHFS" "neurodevelopmental delay" "0000321933" "05611" "00431333" "00006" "Familial, autosomal recessive" "30m" "see paper; ..., global development delay; 8m-sit,308m-walk; 30 months babbling, no speech; normal behavior; neurologic features; hypotonia; no muscle weakness; seizures; no pyramidal signs; ataxia; unremarkable; prominent ears; normal eyes; no high arched narrow palate; normal nose; no thin upper lip; no pointy chin; normal teeth; skin abnormalities; dry skin, eczema; normal hair growth; exotropia; no hypermetropia; normal vision; gastro-intestinal abnormalities; some feeding difficulties; early obesity; abnormalities extremities; hypermobility; deep palmar creases" "" "" "" "" "" "" "" "NEDHFS" "neurodevelopmental delay" ## Screenings ## Do not remove or alter this header ## ## Count = 6 "{{id}}" "{{individualid}}" "{{variants_found}}" "{{owned_by}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "{{Screening/Technique}}" "{{Screening/Template}}" "{{Screening/Tissue}}" "{{Screening/Remarks}}" "0000000209" "00000208" "1" "00037" "00001" "2012-09-13 12:02:03" "" "" "SEQ-NG-I" "DNA" "" "" "0000000210" "00000209" "1" "00037" "00001" "2012-09-13 12:09:36" "" "" "SEQ-NG-I" "DNA" "" "" "0000432742" "00431330" "1" "00006" "00006" "2023-02-08 20:43:15" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000432743" "00431331" "1" "00006" "00006" "2023-02-08 20:43:15" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000432744" "00431332" "1" "00006" "00006" "2023-02-08 20:43:15" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000432745" "00431333" "1" "00006" "00006" "2023-02-08 20:43:15" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 0 ## 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 = 15 "{{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}}" "0000002541" "3" "50" "11" "74066503" "74066503" "dup" "0" "00037" "PGM2L1_000009" "g.74066503dup" "" "" "" "" "" "Germline" "" "" "" "" "" "g.74355458dup" "" "VUS" "" "0000005025" "3" "50" "11" "74065411" "74065411" "subst" "0" "00037" "PGM2L1_000006" "g.74065411G>T" "" "" "" "" "" "Germline" "" "" "" "" "" "g.74354366G>T" "" "VUS" "" "0000005026" "3" "50" "11" "74066337" "74066337" "subst" "0" "00037" "PGM2L1_000003" "g.74066337A>G" "" "" "" "" "" "Germline" "" "" "" "" "" "g.74355292A>G" "" "VUS" "" "0000005027" "0" "50" "11" "74066427" "74066427" "subst" "0" "00037" "PGM2L1_000005" "g.74066427G>A" "" "" "" "" "" "Germline" "" "" "" "" "" "g.74355382G>A" "" "VUS" "" "0000010546" "0" "50" "11" "74066503" "74066503" "dup" "0" "00037" "PGM2L1_000009" "g.74066503dup" "" "" "" "" "" "Germline" "" "" "" "" "" "g.74355458dup" "" "VUS" "" "0000010547" "0" "50" "11" "74066616" "74066624" "del" "0" "00037" "PGM2L1_000008" "g.74066616_74066624del" "" "" "" "" "" "Germline" "" "" "" "" "" "g.74355571_74355579del" "" "VUS" "" "0000012970" "0" "50" "11" "74065411" "74065411" "subst" "0" "00037" "PGM2L1_000006" "g.74065411G>T" "" "" "" "" "" "Germline" "" "" "" "" "" "g.74354366G>T" "" "VUS" "" "0000012971" "3" "50" "11" "74066337" "74066337" "subst" "0" "00037" "PGM2L1_000003" "g.74066337A>G" "" "" "" "" "" "Germline" "" "" "" "" "" "g.74355292A>G" "" "VUS" "" "0000012972" "0" "50" "11" "74066586" "74066586" "subst" "0" "00037" "PGM2L1_000001" "g.74066586G>A" "" "" "" "" "" "Germline" "" "" "" "" "" "g.74355541G>A" "" "VUS" "" "0000890176" "0" "50" "11" "74057837" "74057837" "subst" "4.87349E-5" "02325" "PGM2L1_000010" "g.74057837C>T" "" "" "" "PGM2L1(NM_173582.6):c.977G>A (p.R326Q)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000918321" "3" "90" "11" "74053589" "74053590" "del" "0" "00006" "PGM2L1_000011" "g.74053589_74053590del" "" "{PMID:Morova 2021:33979636}" "" "1548_1549delTC" "" "Germline" "" "" "0" "" "" "g.74342544_74342545del" "" "pathogenic (recessive)" "" "0000918322" "21" "90" "11" "74109160" "74109160" "del" "0" "00006" "PGM2L1_000015" "g.74109160del" "" "{PMID:Morova 2021:33979636}" "" "51delC" "" "Germline" "" "" "0" "" "" "g.74398115del" "" "pathogenic (recessive)" "" "0000918323" "3" "90" "11" "74085567" "74085567" "subst" "0" "00006" "PGM2L1_000014" "g.74085567G>A" "" "{PMID:Morova 2021:33979636}" "" "" "" "Germline" "" "" "0" "" "" "g.74374522G>A" "" "pathogenic (recessive)" "" "0000918324" "3" "90" "11" "74054398" "74054398" "subst" "4.14436E-6" "00006" "PGM2L1_000012" "g.74054398C>A" "" "{PMID:Morova 2021:33979636}" "" "" "" "Germline" "" "" "0" "" "" "g.74343353C>A" "" "pathogenic (recessive)" "" "0000918325" "11" "90" "11" "74056621" "74056621" "del" "0" "00006" "PGM2L1_000013" "g.74056621del" "" "{PMID:Morova 2021:33979636}" "" ".1115delA" "" "Germline" "" "" "0" "" "" "g.74345576del" "" "pathogenic (recessive)" "" ## 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 PGM2L1 ## Count = 15 "{{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}}" "0000002541" "00001200" "50" "556" "-3881" "556" "-3881" "c.556-3881dup" "r.(=)" "p.(=)" "" "0000005025" "00001200" "50" "556" "-2790" "556" "-2790" "c.556-2790C>A" "r.(=)" "p.(=)" "" "0000005026" "00001200" "50" "556" "-3716" "556" "-3716" "c.556-3716T>C" "r.(=)" "p.(=)" "" "0000005027" "00001200" "50" "556" "-3806" "556" "-3806" "c.556-3806C>T" "r.(=)" "p.(=)" "" "0000010546" "00001200" "50" "556" "-3881" "556" "-3881" "c.556-3881dup" "r.(=)" "p.(=)" "" "0000010547" "00001200" "50" "556" "-3986" "556" "-3978" "c.556-3986_556-3978del" "r.(=)" "p.(=)" "" "0000012970" "00001200" "50" "556" "-2790" "556" "-2790" "c.556-2790C>A" "r.(=)" "p.(=)" "" "0000012971" "00001200" "50" "556" "-3716" "556" "-3716" "c.556-3716T>C" "r.(=)" "p.(=)" "" "0000012972" "00001200" "50" "556" "-3965" "556" "-3965" "c.556-3965C>T" "r.(=)" "p.(=)" "" "0000890176" "00001200" "50" "977" "0" "977" "0" "c.977G>A" "r.(?)" "p.(Arg326Gln)" "" "0000918321" "00001200" "90" "1548" "0" "1549" "0" "c.1548_1549del" "r.(?)" "p.(Pro517LysfsTer19)" "" "0000918322" "00001200" "90" "51" "0" "51" "0" "c.51del" "r.(?)" "p.(Tyr18ThrfsTer36)" "" "0000918323" "00001200" "90" "172" "0" "172" "0" "c.172C>T" "r.(?)" "p.(Arg58Ter)" "" "0000918324" "00001200" "90" "1282" "0" "1282" "0" "c.1282G>T" "r.(?)" "p.(Glu428Ter)" "" "0000918325" "00001200" "90" "1115" "0" "1115" "0" "c.1115del" "r.(?)" "p.(Asn372IlefsTer8)" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 14 "{{screeningid}}" "{{variantid}}" "0000000209" "0000002541" "0000000209" "0000005025" "0000000209" "0000005026" "0000000209" "0000005027" "0000000210" "0000010546" "0000000210" "0000010547" "0000000210" "0000012970" "0000000210" "0000012971" "0000000210" "0000012972" "0000432742" "0000918321" "0000432743" "0000918322" "0000432743" "0000918325" "0000432744" "0000918323" "0000432745" "0000918324"