### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = SHMT2) # 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}}" "SHMT2" "serine hydroxymethyltransferase 2 (mitochondrial)" "12" "q12-q14" "unknown" "NG_029163.1" "UD_132118616966" "" "https://www.LOVD.nl/SHMT2" "" "1" "10852" "6472" "138450" "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/SHMT2_codingDNA.html" "1" "" "" "-1" "" "-1" "00001" "2013-05-03 00:00:00" "00006" "2020-11-01 12:03:13" "00000" "2026-01-20 18:57:21" ## 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}}" "00018891" "SHMT2" "transcript variant 1" "001" "NM_005412.5" "" "NP_005403.2" "" "" "" "-206" "2089" "1515" "57623356" "57628718" "" "0000-00-00 00:00:00" "" "" ## Diseases ## Do not remove or alter this header ## ## Count = 1 "{{id}}" "{{symbol}}" "{{name}}" "{{inheritance}}" "{{id_omim}}" "{{tissues}}" "{{features}}" "{{remarks}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "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 = 1 "{{geneid}}" "{{diseaseid}}" "SHMT2" "05611" ## Individuals ## Do not remove or alter this header ## ## Count = 5 "{{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}}" "00316020" "" "" "" "2" "" "00006" "{PMID:Garcia-Cazorla 2020: 33015733}" "2-generation family, 2 affected brothers, unaffected heterozygous carrier parents" "M" "yes" "" "" "0" "" "" "" "Fam1Pat1" "00316021" "" "" "00316020" "1" "" "00006" "{PMID:Garcia-Cazorla 2020: 33015733}" "brother" "M" "yes" "" "" "0" "" "" "" "Fam1Pat2" "00316022" "" "" "" "1" "" "00006" "{PMID:Garcia-Cazorla 2020: 33015733}" "2-generation family, 1 affected, unaffected heterozygous carrier parents" "F" "" "" "" "0" "" "" "" "Fam2Pat3" "00316023" "" "" "" "1" "" "00006" "{PMID:Garcia-Cazorla 2020: 33015733}" "2-generation family, 1 affected, unaffected heterozygous carrier parents" "F" "" "" "" "0" "" "" "" "Fam3Pat4" "00316024" "" "" "" "1" "" "00006" "{PMID:Garcia-Cazorla 2020: 33015733}" "2-generation family, 1 affected, unaffected heterozygous carrier parents" "M" "" "" "" "0" "" "" "" "Fam4Pat5" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 5 "{{individualid}}" "{{diseaseid}}" "00316020" "05611" "00316021" "05611" "00316022" "05611" "00316023" "05611" "00316024" "05611" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 05611 ## Count = 5 "{{id}}" "{{diseaseid}}" "{{individualid}}" "{{owned_by}}" "{{Phenotype/Inheritance}}" "{{Phenotype/Age}}" "{{Phenotype/Additional}}" "{{Phenotype/Age/Onset}}" "{{Phenotype/Age/Diagnosis}}" "{{Phenotype/Onset}}" "{{Phenotype/Enzyme/CPK}}" "{{Phenotype/Heart/Myocardium}}" "{{Phenotype/Lung}}" "{{Phenotype/Diagnosis/Definite}}" "{{Phenotype/Diagnosis/Initial}}" "0000239765" "05611" "00316020" "00006" "Familial, autosomal recessive" "10y" "birth weight 3630 gr (0.7 SD), OFC 32.3 cm (-2.1 SD); 10y-OFC 51.5 cm (-2.1 SD); severe intellectual disability; microcephaly detected during pregnancy; hypotonia at birth; first words-2y, walk-3.5y.; anxiety; attention deficit hyperactivity disorder-like; spasticity lower limbs, with increased deep tendon reflexes and extensor reflex; no ataxia, no dysmetria; distal neuroaxonal impairment; MRI brain corpus callosum hypoplasia, bilateral Perisylvian polymicrogyria; 5y-hypertrophic cardiomyopathy; arched eyebrows, thin upper lip, long philtrum, low-set thumbs, 2-3 toe syndactyly; conjunctival hyperemia, ocular movements: slow saccades, drooling, orofacial dyspraxia" "" "" "" "" "" "" "" "" "0000239766" "05611" "00316021" "00006" "Familial, autosomal recessive" "20y" "birth weight 3320 gr (0.02 SD), OFC 32 cm (-2.4 SD); 20y-OFC 54.5 cm (1.3 SD); severe intellectual disability; microcephaly at birth; hypertonia extremities; first words-28m, walks-3.5y.; anxiety; hand stereotypies, autistic traits, short attention span, agressive bursts; spasticity lower limbs, with increased deep tendon reflexes and extensor reflex, scissors gait; truncal ataxia, spastic-dyspraxic gait, dysmetria; intention tremor, dystonicmovements; progressive axonal and sensory neuropathy; MRI brain corpus callosum hypoplasia, bilateral Perisylvian polymicrogyria; 16y-hypertrophic cardiomyopathy with left moderate ventricular dysfunction, ejection fraction of 0.40; arched eyebrows, low-set thumbs, 2-3 toe syndactyly; conjunctival hyperemia, scoliosis, ocular movements: slow saccades, drooling, orofacial dyspraxia eeg bifrontal discharges without clinical seizures" "" "" "" "" "" "" "" "" "0000239767" "05611" "00316022" "00006" "Familial, autosomal recessive" "19y" "birth weight 2578 gr (-1.5 SD), OFC 28.5 cm (-3 SD); 19y-OFC 53.5 cm (-1.5 SD); mild-moderate intellectual disability; microcephaly detected during pregnancy; sits9m, crawl-17m, walks26m; anxiety; attention deficit hyperactivity disorder-like; hypertonia limbs, hyperreflexia limbs; dysmetria; intention tremor, hand stereotypies; MRI brain hypoplasia, dysmorphy corpus callosum, unilateral Perisylvian polymicrogyria; 3y-hypertrophic cardiomyopathy; short philtrum, small downturned mouth digitalized thumbs; subclavian vascular ring, cyclic vomiting, strabismus right eye, tonic upward eye movement, mild amblyopia" "" "" "" "" "" "" "" "" "0000239768" "05611" "00316023" "00006" "Familial, autosomal recessive" "12y" "birth weight 2840 gr (0.8 SD), OFC 31.5 cm (-2.3 SD); 12y-OFC 51 cm (-2.43 SD); moderate intellectual disability; microcephaly detected during pregnancy; holds head-4m, sit-8m, first words-14m, walk-24m; no anxiety; attention deficit hyperactivity disorder-like, dysfunctional adaptative behavior; hypertonia limbs, hyperreflexia limbs, spastic gait; spastic-dyspraxic gait, dysmetria, SARA scale 5; intention tremor, mild hypokinesia, bradykinesia; 9y-nerve conduction normal; MRI brain corpus callosum hypoplasia, unilateral Perisylvian polymicrogyria; 9y-severe hypertrophic cardiomyopathy; heart transplantation; arched eyebrows, thin upper lip,low-set thumbs, 2-3 toe syndactyly; expressive language disorder" "" "" "" "" "" "" "" "" "0000239769" "05611" "00316024" "00006" "Familial, autosomal recessive" "02y" "birth weight 2700 gr (-1.4 SD), OFC 31.5 cm (-2.9 SD);2y OFC 46cm (-3SD); severe intellectual disability; microcephaly detected during pregnancy; holds head-12m, no sitting, no speech; spastic tetraplegia; MRI brain thin corpus callosum, ventriculomegaly; atrial septum defects, ostium secondum; facial diplegia, retrognathia, bifid uvula, closed hands, adductus thumbs; mild scoliosis, hip dislocation, divergent strabismus" "" "" "" "" "" "" "" "" ## Screenings ## Do not remove or alter this header ## ## Count = 5 "{{id}}" "{{individualid}}" "{{variants_found}}" "{{owned_by}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "{{Screening/Technique}}" "{{Screening/Template}}" "{{Screening/Tissue}}" "{{Screening/Remarks}}" "0000317202" "00316020" "1" "00006" "00006" "2020-11-01 12:39:14" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000317203" "00316021" "1" "00006" "00006" "2020-11-01 12:39:14" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000317204" "00316022" "1" "00006" "00006" "2020-11-01 12:39:14" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000317205" "00316023" "1" "00006" "00006" "2020-11-01 12:39:14" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000317206" "00316024" "1" "00006" "00006" "2020-11-01 12:39:14" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 5 "{{screeningid}}" "{{geneid}}" "0000317202" "SHMT2" "0000317203" "SHMT2" "0000317204" "SHMT2" "0000317205" "SHMT2" "0000317206" "SHMT2" ## 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 = 21 "{{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}}" "0000349761" "0" "50" "12" "57638105" "57638105" "subst" "8.53027E-5" "02327" "STAC3_000001" "g.57638105C>G" "" "" "" "" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.57244322C>G" "" "VUS" "" "0000548766" "0" "50" "12" "57626547" "57626547" "subst" "4.06669E-6" "01943" "SHMT2_000001" "g.57626547G>T" "" "" "" "SHMT2(NM_001166357.1):c.715G>T (p.A239S)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.57232764G>T" "" "VUS" "" "0000548767" "0" "50" "12" "57637942" "57637942" "del" "0" "01943" "NDUFA4L2_000002" "g.57637942del" "" "" "" "STAC3(NM_145064.2):c.925delC (p.R309Vfs*5)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "g.57244159del" "" "VUS" "" "0000699407" "3" "90" "12" "57628124" "57628124" "subst" "0" "00006" "SHMT2_000008" "g.57628124C>G" "" "{PMID:Garcia-Cazorla 2020: 33015733}" "" "" "" "Germline" "" "" "0" "" "" "g.57234341C>G" "" "pathogenic (recessive)" "" "0000699408" "2" "90" "12" "57628124" "57628124" "subst" "0" "00006" "SHMT2_000008" "g.57628124C>G" "" "{PMID:Garcia-Cazorla 2020: 33015733}" "" "" "" "Germline" "" "" "0" "" "" "g.57234341C>G" "" "pathogenic (recessive)" "" "0000699409" "11" "90" "12" "57627528" "57627533" "delins" "0" "00006" "SHMT2_000002" "g.57627528_57627533delinsA" "" "{PMID:Garcia-Cazorla 2020: 33015733}" "" "" "" "Germline" "" "" "0" "" "" "g.57233745_57233750delinsA" "" "pathogenic (recessive)" "" "0000699410" "11" "90" "12" "57625653" "57625653" "subst" "4.10196E-6" "00006" "SHMT2_000003" "g.57625653C>T" "" "{PMID:Garcia-Cazorla 2020: 33015733}" "" "" "" "Germline" "" "" "0" "" "" "g.57231870C>T" "" "pathogenic (recessive)" "" "0000699411" "11" "90" "12" "57626038" "57626038" "subst" "0" "00006" "SHMT2_000004" "g.57626038C>G" "" "{PMID:Garcia-Cazorla 2020: 33015733}" "" "" "" "Germline" "" "" "0" "" "" "g.57232255C>G" "" "pathogenic (recessive)" "" "0000699412" "21" "90" "12" "57627675" "57627675" "subst" "2.43714E-5" "00006" "SHMT2_000006" "g.57627675G>A" "" "{PMID:Garcia-Cazorla 2020: 33015733}" "" "" "" "Germline" "" "" "0" "" "" "g.57233892G>A" "" "pathogenic (recessive)" "" "0000699413" "21" "90" "12" "57627810" "57627810" "subst" "0" "00006" "SHMT2_000007" "g.57627810A>C" "" "{PMID:Garcia-Cazorla 2020: 33015733}" "" "" "" "Germline" "" "" "0" "" "" "g.57234027A>C" "" "pathogenic (recessive)" "" "0000699414" "21" "90" "12" "57627543" "57627543" "subst" "0" "00006" "SHMT2_000005" "g.57627543A>G" "" "{PMID:Garcia-Cazorla 2020: 33015733}" "" "" "" "Germline" "" "" "0" "" "" "g.57233760A>G" "" "pathogenic (recessive)" "" "0000724157" "0" "50" "12" "57638123" "57638123" "subst" "2.0314E-5" "01804" "NDUFA4L2_000003" "g.57638123T>C" "" "" "" "STAC3(NM_001286256.1):c.716A>G (p.(Asp239Gly))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0000724158" "0" "30" "12" "57639002" "57639002" "subst" "0.0107515" "01804" "NDUFA4L2_000004" "g.57639002G>A" "" "" "" "STAC3(NM_001286256.1):c.487-8C>T (p.(=))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000805868" "0" "30" "12" "57627779" "57627779" "subst" "0.000134006" "01943" "NDUFA4L2_000005" "g.57627779G>A" "" "" "" "SHMT2(NM_001166357.1):c.1217-7G>A" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000950004" "0" "30" "12" "57637604" "57637604" "subst" "0.00293885" "02326" "NDUFA4L2_000006" "g.57637604C>T" "" "" "" "STAC3(NM_145064.3):c.1086G>A (p.E362=)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0001039387" "0" "30" "12" "57626367" "57626367" "subst" "7.74107E-5" "01804" "NDUFA4L2_000007" "g.57626367G>T" "" "" "" "SHMT2(NM_005412.6):c.717+9G>T" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0001039388" "0" "50" "12" "57637889" "57637889" "subst" "4.06213E-5" "01804" "NDUFA4L2_000008" "g.57637889G>C" "" "" "" "STAC3(NM_145064.3):c.978C>G (p.(Ile326Met))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0001054377" "0" "30" "12" "57626075" "57626075" "subst" "5.27906E-5" "01804" "NDUFA4L2_000009" "g.57626075C>T" "" "" "" "SHMT2(NM_005412.6):c.594C>T (p.(Asn198=))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0001054378" "0" "50" "12" "57626627" "57626627" "subst" "0" "01804" "NDUFA4L2_000010" "g.57626627G>C" "" "" "" "SHMT2(NM_005412.6):c.857+1G>C" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0001054379" "0" "50" "12" "57638703" "57638703" "subst" "0" "01804" "NDUFA4L2_000011" "g.57638703T>C" "" "" "" "STAC3(NM_145064.3):c.716A>G (p.(Asp239Gly))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0001065775" "0" "50" "12" "57626329" "57626329" "subst" "1.62446E-5" "02325" "NDUFA4L2_000012" "g.57626329C>T" "" "" "" "" "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 SHMT2 ## Count = 21 "{{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}}" "0000349761" "00018891" "50" "11476" "0" "11476" "0" "c.*9961C>G" "r.(=)" "p.(=)" "" "0000548766" "00018891" "50" "778" "0" "778" "0" "c.778G>T" "r.(?)" "p.(Ala260Ser)" "" "0000548767" "00018891" "50" "11313" "0" "11313" "0" "c.*9798del" "r.(?)" "p.(=)" "" "0000699407" "00018891" "90" "1495" "0" "1495" "0" "c.1495C>G" "r.(?)" "p.(Pro499Ala)" "" "0000699408" "00018891" "90" "1495" "0" "1495" "0" "c.1495C>G" "r.(?)" "p.(Pro499Ala)" "" "0000699409" "00018891" "90" "1124" "-4" "1125" "0" "c.1124-4_1125delinsA" "r.1124_1126del" "p.Gly375del" "" "0000699410" "00018891" "90" "469" "0" "469" "0" "c.469C>T" "r.(?)" "p.(Pro157Ser)" "" "0000699411" "00018891" "90" "557" "0" "557" "0" "c.557C>G" "r.(?)" "p.(Thr186Arg)" "" "0000699412" "00018891" "90" "1267" "0" "1267" "0" "c.1267G>A" "r.(?)" "p.(Gly423Ser)" "" "0000699413" "00018891" "90" "1304" "0" "1304" "0" "c.1304A>C" "r.(?)" "p.(Gln435Pro)" "" "0000699414" "00018891" "90" "1135" "0" "1135" "0" "c.1135A>G" "r.(?)" "p.(Asn379Asp)" "" "0000724157" "00018891" "50" "11494" "0" "11494" "0" "c.*9979T>C" "r.(=)" "p.(=)" "" "0000724158" "00018891" "30" "12373" "0" "12373" "0" "c.*10858G>A" "r.(=)" "p.(=)" "" "0000805868" "00018891" "30" "1280" "-7" "1280" "-7" "c.1280-7G>A" "r.(=)" "p.(=)" "" "0000950004" "00018891" "30" "10975" "0" "10975" "0" "c.*9460C>T" "r.(=)" "p.(=)" "" "0001039387" "00018891" "30" "717" "9" "717" "9" "c.717+9G>T" "r.(=)" "p.(=)" "" "0001039388" "00018891" "50" "11260" "0" "11260" "0" "c.*9745G>C" "r.(=)" "p.(=)" "" "0001054377" "00018891" "30" "594" "0" "594" "0" "c.594C>T" "r.(?)" "p.(=)" "" "0001054378" "00018891" "50" "857" "1" "857" "1" "c.857+1G>C" "r.spl?" "p.?" "" "0001054379" "00018891" "50" "12074" "0" "12074" "0" "c.*10559T>C" "r.(=)" "p.(=)" "" "0001065775" "00018891" "50" "688" "0" "688" "0" "c.688C>T" "r.(?)" "p.(Arg230Cys)" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 8 "{{screeningid}}" "{{variantid}}" "0000317202" "0000699407" "0000317203" "0000699408" "0000317204" "0000699409" "0000317204" "0000699412" "0000317205" "0000699410" "0000317205" "0000699413" "0000317206" "0000699411" "0000317206" "0000699414"