### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = TM2D3) # 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}}" "TM2D3" "TM2 domain containing 3" "15" "q26.3" "unknown" "NC_000015.9" "UD_132378476542" "" "https://www.LOVD.nl/TM2D3" "" "1" "24128" "80213" "610014" "1" "1" "1" "1" "Establishment of this gene variant database (LSDB) was performed by Johan den Dunnen, supported by Global Variome." "" "" "" "1" "" "" "-1" "" "-1" "00001" "2013-05-03 00:00:00" "00006" "2025-07-07 12:10:44" "00006" "2025-07-07 15:07:41" ## 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}}" "00021200" "TM2D3" "transcript variant 1" "002" "NM_078474.2" "" "NP_510883.2" "" "" "" "-30" "1377" "744" "102192594" "102182049" "" "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}}" "00139" "ID" "intellectual disability (ID)" "" "" "" "" "" "00084" "2013-06-04 18:18:07" "00006" "2015-02-09 10:02:49" "04254" "CLP" "cleft lip, cleft palate (CLP)" "" "" "" "" "" "00006" "2015-05-08 09:59:28" "00006" "2015-05-08 10:00:15" "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}}" "TM2D3" "05611" ## 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}}" "00231412" "" "" "" "6" "" "03278" "{PMID:Cox 2019:31215115}" "4-generation family, 6 affected (3F, 3M)" "F;M" "" "United States" "" "0" "" "" "" "Fam4527" "00318040" "" "" "" "1" "" "00006" "{PMID:Riazuddin 2017:27457812}" "" "" "yes" "Pakistan" "" "0" "" "" "Punjabi" "PKMR325" "00466014" "" "" "" "1" "" "00006" "{PMID:Gabillard-Lefort 2025:40449487}, {DOI:Gabillard-Lefort 2025:10.1016/j.ajhg.2025.05.004}" "2-generation family, 1 affected, unaffected heterozygous carrier parents" "M" "no" "France" "" "0" "" "" "" "Fam1PatII1" "00466015" "" "" "" "1" "" "00006" "{PMID:Gabillard-Lefort 2025:40449487}, {DOI:Gabillard-Lefort 2025:10.1016/j.ajhg.2025.05.004}" "2-generation family, 1 affected, unaffected heterozygous carrier parents" "M" "no" "France" "" "0" "" "" "" "Fam2PatII1" "00466016" "" "" "" "1" "" "00006" "{PMID:Gabillard-Lefort 2025:40449487}, {DOI:Gabillard-Lefort 2025:10.1016/j.ajhg.2025.05.004}" "2-generation family, 1 affected, unaffected heterozygous carrier parents" "F" "no" "Italy" "" "0" "" "" "" "Fam3PatII1" "00466017" "" "" "" "1" "" "00006" "{PMID:Gabillard-Lefort 2025:40449487}, {DOI:Gabillard-Lefort 2025:10.1016/j.ajhg.2025.05.004}" "2-generation family, 1 affected, unaffected heterozygous carrier parents" "F" "no" "United States" "" "0" "" "" "" "Fam4PatII1" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 6 "{{individualid}}" "{{diseaseid}}" "00231412" "04254" "00318040" "00139" "00466014" "05611" "00466015" "05611" "00466016" "05611" "00466017" "05611" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 00139, 04254, 05611 ## 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}}" "0000173804" "04254" "00231412" "03278" "Familial, autosomal dominant" "" "vertebral hyper segmentation (HP:0003422), rib hyper segmentation (HP:0006655)" "" "" "" "" "" "" "" "" "" "0000241824" "00139" "00318040" "00006" "Familial, autosomal recessive" "" "IV:1 Mild ID, aggressive, dental carries; IV:2 severe ID, spasticity, aggressive, speech and walking delay CMS." "" "" "" "" "" "" "" "" "intellectual disability" "0000351399" "05611" "00466014" "00006" "Familial, autosomal recessive" "6y6m" "see paper; ..., intrauterine growth retardation; birth-38w, 1,870g, 46cm, 32cm; height -3 SD, weight -2.5 SD, OFC -5 SD; severe developmental delay; not walking; speech vocalization; hypertonia, dystonia; anxiety, agitation, relational disorder; no seizures; MRI brain 18m/36ym-global hypotrophy with small frontal lobes; mild pyelocaliceal dilatation; patent ductus arteriosus, patent foramen ovale; hypermetropia; scrotal hypoplasia" "" "" "" "" "" "" "" "" "neurodevelopmental delay" "0000351400" "05611" "00466015" "00006" "Familial, autosomal recessive" "6y" "see paper; ..., intrauterine growth retardation, kidney malformation, polyvalvular dysplasia; birth-35w, 1,780g, 41cm, 30cm; height -3.3 SD, weight -2.5 SD, OFC -3.6 SD; severe developmental delay; 4y-walk with support; speech vocalization; hypertonia, dystonia; anxiety, autistic features; 1y6m-seizures; MRI brain 5y-small frontal lobes, abnormal gyration, thick corpus callosum; horseshoe kidney; polyvalvular dysplasia, ventricular septal defect; hypermetropia, strabismus; scrotal hypoplasia, cryptorchidism" "" "" "" "" "" "" "" "" "neurodevelopmental delay" "0000351401" "05611" "00466016" "00006" "Familial, autosomal recessive" "5y6m" "see paper; ..., polyhydramnios, fetal kidney malformation; birth-36w, 2,720g; height +1.3 SD, weight -0.5 SD, OFC -2.5 SD; severe developmental delay; 3y-walk with support; speech vocalization, bi-syllabic words; hemiplegic episodes; agitation; 2m-seizures, alternating hemiplegia; MRI brain 1y/5y-abnormal frontal folding, vermis hypoplasia; horseshoe kidney; three ventricular septal defects, vena cava duplication; no ophthalmologic features; no reproductive organ anomaly" "" "" "" "" "" "" "" "" "neurodevelopmental delay" "0000351402" "05611" "00466017" "00006" "Familial, autosomal recessive" "26y" "see paper; ..., decreased fetal activity; birth-36w, 25th p, 50th p, 10th p; height +0.3 SD, weight -1.8 SD, OFC -4 SD; severe developmental delay; 2y-walk, wide-based gait; speech vocalization; hypertonia; anxiety, agitation, autistic features; no seizures; CT scan brain 3y-pineal cyst; abdominal ultrasound normal; ventricular septal defect; strabismus, legal blindness; no reproductive organ anomaly" "" "" "" "" "" "" "" "" "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}}" "0000232511" "00231412" "1" "03278" "03278" "2019-05-02 06:00:24" "" "" "SEQ-NG" "DNA" "" "" "0000319222" "00318040" "1" "00006" "00006" "2020-11-05 17:52:36" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000467665" "00466014" "1" "00006" "00006" "2025-07-07 15:05:37" "00006" "2025-07-07 15:07:08" "RT-PCR;SEQ;SEQ-NG" "DNA;RNA" "" "WES" "0000467666" "00466015" "1" "00006" "00006" "2025-07-07 15:05:37" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000467667" "00466016" "1" "00006" "00006" "2025-07-07 15:05:37" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000467668" "00466017" "1" "00006" "00006" "2025-07-07 15:05:37" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 2 "{{screeningid}}" "{{geneid}}" "0000232511" "GDF11" "0000319222" "TM2D3" ## 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 = 10 "{{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}}" "0000480529" "0" "70" "15" "102182739" "102182739" "subst" "2.04802E-5" "03278" "TM2D3_000001" "g.102182739G>T" "" "{PMID:Cox 2019:31215115}" "" "" "" "Germline" "" "" "0" "" "" "g.101642536G>T" "" "VUS" "" "0000701886" "3" "50" "15" "102182749" "102182749" "subst" "4.10243E-6" "00006" "TM2D3_000002" "g.102182749G>A" "" "{PMID:Riazuddin 2017:27457812}" "" "" "" "Germline" "" "" "0" "" "" "g.101642546G>A" "" "VUS" "" "0000806569" "0" "50" "15" "102182738" "102182738" "subst" "4.50554E-5" "01943" "TM2D3_000003" "g.102182738C>T" "" "" "" "TM2D3(NM_078474.3):c.688G>A (p.V230I)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "VUS" "" "0001045560" "11" "70" "15" "102185365" "102185365" "subst" "0" "00006" "TM2D3_000004" "g.102185365C>T" "" "{PMID:Gabillard-Lefort 2025:40449487}, {DOI:Gabillard-Lefort 2025:10.1016/j.ajhg.2025.05.004}" "" "" "variant has no effect on splicing" "Germline" "" "" "0" "" "" "g.101645162C>T" "SCV005387825" "likely pathogenic (recessive)" "" "0001045561" "21" "70" "15" "102185365" "102185365" "subst" "0" "00006" "TM2D3_000004" "g.102185365C>T" "" "{PMID:Gabillard-Lefort 2025:40449487}, {DOI:Gabillard-Lefort 2025:10.1016/j.ajhg.2025.05.004}" "" "" "" "Germline" "" "" "0" "" "" "g.101645162C>T" "SCV005387825" "likely pathogenic (recessive)" "" "0001045562" "3" "70" "15" "102185365" "102185365" "subst" "0" "00006" "TM2D3_000004" "g.102185365C>T" "" "{PMID:Gabillard-Lefort 2025:40449487}, {DOI:Gabillard-Lefort 2025:10.1016/j.ajhg.2025.05.004}" "" "" "" "Germline" "" "" "0" "" "" "g.101645162C>T" "SCV005387825" "likely pathogenic (recessive)" "" "0001045563" "21" "70" "15" "102182749" "102182749" "subst" "4.10243E-6" "00006" "TM2D3_000002" "g.102182749G>A" "" "{PMID:Gabillard-Lefort 2025:40449487}, {DOI:Gabillard-Lefort 2025:10.1016/j.ajhg.2025.05.004}" "" "" "" "Germline" "" "" "0" "" "" "g.101642546G>A" "SCV005387826" "likely pathogenic (recessive)" "" "0001045564" "21" "70" "15" "102192558" "102192558" "subst" "0" "00006" "TM2D3_000007" "g.102192558C>A" "" "{PMID:Gabillard-Lefort 2025:40449487}, {DOI:Gabillard-Lefort 2025:10.1016/j.ajhg.2025.05.004}" "" "" "" "Germline" "" "" "0" "" "" "g.101652355C>A" "SCV005387827" "likely pathogenic (recessive)" "" "0001045565" "11" "70" "15" "102191915" "102191915" "dup" "0" "00006" "TM2D3_000006" "g.102191915dup" "" "{PMID:Gabillard-Lefort 2025:40449487}, {DOI:Gabillard-Lefort 2025:10.1016/j.ajhg.2025.05.004}" "" "" "" "Germline" "" "" "0" "" "" "g.101651712dup" "SCV005387828" "likely pathogenic (recessive)" "" "0001045566" "11" "70" "15" "102182681" "102215940" "del" "0" "00006" "TM2D3_000005" "g.(?_102182681)_(102215940_?)del" "" "{PMID:Gabillard-Lefort 2025:40449487}, {DOI:Gabillard-Lefort 2025:10.1016/j.ajhg.2025.05.004}" "" "chr15:102182681–102215940 (GRCh37)" "del15q26.3 (33 kb)" "Germline" "" "" "0" "" "" "g.(?_101642478)_(101675737_?)del" "" "likely 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 TM2D3 ## Count = 10 "{{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}}" "0000480529" "00021200" "70" "687" "0" "687" "0" "c.687C>A" "r.(?)" "p.(Asp229Glu)" "" "0000701886" "00021200" "50" "677" "0" "677" "0" "c.677C>T" "r.(?)" "p.(Thr226Met)" "" "0000806569" "00021200" "50" "688" "0" "688" "0" "c.688G>A" "r.(?)" "p.(Val230Ile)" "" "0001045560" "00021200" "70" "503" "0" "503" "0" "c.503G>A" "r.503G>A" "p.Gly168Asp" "" "0001045561" "00021200" "70" "503" "0" "503" "0" "c.503G>A" "r.(?)" "p.(Gly168Asp)" "" "0001045562" "00021200" "70" "503" "0" "503" "0" "c.503G>A" "r.(?)" "p.(Gly168Asp)" "" "0001045563" "00021200" "70" "677" "0" "677" "0" "c.677C>T" "r.(?)" "p.(Thr226Met)" "" "0001045564" "00021200" "70" "7" "0" "7" "0" "c.7G>T" "r.(?)" "p.(Gly3Ter)" "" "0001045565" "00021200" "70" "153" "0" "153" "0" "c.153dup" "r.(?)" "p.(Val52SerfsTer9)" "" "0001045566" "00021200" "70" "" "0" "" "0" "c.(?_-23376)_(*1_?)del" "r.0" "p.0" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 9 "{{screeningid}}" "{{variantid}}" "0000232511" "0000480529" "0000319222" "0000701886" "0000467665" "0001045560" "0000467665" "0001045564" "0000467666" "0001045561" "0000467666" "0001045565" "0000467667" "0001045562" "0000467668" "0001045563" "0000467668" "0001045566"