### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = SCNM1) # 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}}" "SCNM1" "sodium channel modifier 1" "1" "q21.3" "unknown" "NC_000001.10" "UD_136091580524" "" "https://www.LOVD.nl/SCNM1" "" "1" "23136" "79005" "608095" "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/SCNM1_codingDNA.html" "1" "" "" "-1" "" "-1" "00001" "2013-05-03 00:00:00" "00006" "2022-09-13 21:06:44" "00000" "2024-02-26 20:06:56" ## 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}}" "00018528" "SCNM1" "transcript variant 1" "002" "NM_024041.3" "" "NP_076946.1" "" "" "" "-131" "1905" "693" "151138498" "151142773" "" "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}}" "05790" "OFD" "orofaciodigital syndrome (OFD)" "" "" "" "" "" "00006" "2020-07-22 14:56:57" "" "" ## Genes_To_Diseases ## Do not remove or alter this header ## ## Count = 1 "{{geneid}}" "{{diseaseid}}" "SCNM1" "05790" ## Individuals ## Do not remove or alter this header ## ## Count = 4 "{{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}}" "00417197" "" "" "" "2" "" "00006" "{PMID:Iturrate 2022:36084634}, {DOI:Iturrate 2022:10.1016/j.ajhg.2022.08.009}" "2 generation family, 2 affected sisters, unaffected heterozygous carrier parents (first cousins)" "F" "yes" "" "" "0" "" "" "" "Fam1Pat1" "00417198" "" "" "00417197" "1" "" "00006" "{PMID:Iturrate 2022:36084634}, {DOI:Iturrate 2022:10.1016/j.ajhg.2022.08.009}" "sister" "F" "yes" "" "" "0" "" "" "" "Fam1Pat2" "00417199" "" "" "" "1" "" "00006" "{PMID:Iturrate 2022:36084634}, {DOI:Iturrate 2022:10.1016/j.ajhg.2022.08.009}" "2 generation family, 1 affected, unaffected heterozygous carrier parents (2nd cousins)" "F" "yes" "" "" "0" "" "" "" "Fam2Pat3" "00417200" "" "" "" "1" "" "00006" "{PMID:Iturrate 2022:36084634}, {DOI:Iturrate 2022:10.1016/j.ajhg.2022.08.009}" "2 generation family, affected sister/fetus, unaffected heterozygous carrier parents (first cousins)" "F" "yes" "" "" "0" "" "" "" "Fam3Pat4" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 4 "{{individualid}}" "{{diseaseid}}" "00417197" "05790" "00417198" "05790" "00417199" "05790" "00417200" "05790" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 05790 ## Count = 4 "{{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}}" "0000308713" "05790" "00417197" "00006" "Familial, autosomal recessive" "05y01m" "weight 17 kg (-0.45 SD), height 103 cm (-1.12 SD), OFC 50 cm (-0.62 SD); lobulated with nodules; hypodontia (missing lower central incisors), excessive caries; narrow and high-arched; accessory oral frenula; dolichocephaly, frontal bossing; upslanted palpebral fissures; broad nasal bridge, thick alae nasi; protruding, cupped, low-set ears; narrow mouth; median notching of lower lip; retrognathia, horizontal chin crease; bilateral postaxial polydactyly with six fingers on the right and seven fingers on the left (operated); broad, medially deviated halluces, bilateral postaxial polydactyly with six toes; bilateral partial skin syndactyly of the toes; type A brachydactyly of the hands and feet; broad hands, interdigital webbing, single flexion crease in several fingers, broad feet; normal nails; MRI brain ectatic supratentorial ventricular system; no epilepsy; timely acquisition of motor and social skills, delayed speech, normal intellectual performance; mild shortening of forearms, mildly short of tibiae; normal echocardiogram; normal eye examination and fundoscopy; normal abdominal ultrasound, normal pelvic ultrasound" "" "" "" "" "" "" "" "orofaciodigital syndrome" "0000308714" "05790" "00417198" "00006" "Familial, autosomal recessive" "01y10m" "weight 11 kg (-0.49 SD), height 78 cm (-1.23 SD), OFC 46 cm (-0.53 SD); lobulated with nodules; hypodontia (missing lower lateral incisors); narrow and high-arched; accessory oral frenula; broad prominent forehead; hypertelorism, epicanthal folds, strabismus; broad nasal bridge, broad nasal tip; protruding, low-set ears, underfolded helices; downturned corners of the mouth; median notching of upper lip; retrognathia, horizontal chin crease; bilateral pre- and postaxial polydactyly with eight fingers; bilateral pre- and postaxial polydactyly with complete duplication of halluces, with seven toes on the right and eight toes on the left; bilateral partial skin syndactyly of the toes, complete skin syndactyly of digits six to eight on the left; type A brachydactyly of the hands and feet; broad hands, abnormal palmar creases, bilateral Y-shaped metacarpals, very broad feet; normal nails; ; no epilepsy; timely acquisition of motor and social skills; mild shortening of forearms, markedly short tibiae; patent ductus arteriosus, small atrial septal defect; normal eye examination and fundoscopy; normal abdominal ultrasound, normal pelvic ultrasound" "" "" "" "" "" "" "" "orofaciodigital syndrome" "0000308715" "05790" "00417199" "00006" "Familial, autosomal recessive" "07y05m" "weight 34.5 kg (+1.66 SD), height 126.5 cm (+0.41 SD), OFC 51 cm (-0.41 SD); lobulated with nodules; microdontia of upper central incisors; narrow and high arched; serrated and thick alveolar ridge, spoon shaped tongue; high forehead; hypertelorism, epicanthal folds, downslanted palpebral fissures, strabismus (corrected by age); broad nasal bridge, underdeveloped alae nasi, short columella, bifid nasal tip; bifid right ear lobe, low-set ears; narrow mouth, downturned corners of the mouth; thin vermilion of the upper and lower lip; mild retrognathia, horizontal chin crease; low posterior hairline; bilateral postaxial polydactyly with seven fingers on the right (with a shorter, more rudimentary fifth finger in between the well-developed fourth and sixth fingers), and six fingers on the left (a broad sixth finger low-inserted at a right angle to the ulnar side (operated); broad, medially deviated halluces with fused distal phalanges and bifid nails on the right, bilateral postaxial polydactyly (operated); bilateral partial skin syndactyly of the toes; type A brachydactyly of the hands and feet; clinodactyly of right fifth finger with single palmar crease and camptodactyly of left fifth finger, broad and flat feet, bilateral talipes partially corrected by casting; hypoplastic nails more prominent on the feet; MRI brain normal; no epilepsy; timely acquisition of motor skills, normal intellectual performance; short arm span and mild shortening of tibia; normal echocardiogram; normal vision; normal abdominal ultrasound, normal pelvic ultrasound; generalized thin skin with xerosis exacerbating in winter, more prominent over the feet (improved with age)" "" "" "" "" "" "" "" "orofaciodigital syndrome" "0000308716" "05790" "00417200" "00006" "Familial, autosomal recessive" "03y06m" "weight 16.2 kg (+0.65 SD), height 92.4 cm (-1.38 SD), OFC 47 cm (-1.61 SD); tongue nodules; hypodontia (congenital absence of lower central and lateral incisors); soft palate cleft (operated); accessory oral frenula; high forehead; mild epicanthal folds; broad nasal bridge, mildly short nose with anteverted nares; small ear lobes, additional crus of the left antihelix; downturned corners of the mouth; median notching of upper lip; mild retrognathia, horizontal chin crease; bilateral postaxial type A polydactyly with six fingers (operated); broad, medially deviated halluces with broad first metatarsals and bifid and fused distal phalanges, left postaxial hexadactyly (operated); bilateral partial skin syndactyly of the toes; type A brachydactyly of the hands and brachydactyly of the feet; reduced palmar creases, bilateral fifth finger clinodactyly with single flexion crease; broad nails of halluces, small nails of the hands and the remaining digits of the feet; MRI brain normal; no epilepsy; timely acquisition of motor and social skills, delayed speech; short arm span 87 cm (-2.67 SD) with arm span to height ratio of 0.94, lower limbs not evaluated; normal echocardiogram; normal vision; normal abdominal ultrasound, hypoplastic labia minora" "" "" "" "" "" "" "" "orofaciodigital syndrome" ## Screenings ## Do not remove or alter this header ## ## Count = 4 "{{id}}" "{{individualid}}" "{{variants_found}}" "{{owned_by}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "{{Screening/Technique}}" "{{Screening/Template}}" "{{Screening/Tissue}}" "{{Screening/Remarks}}" "0000418484" "00417197" "1" "00006" "00006" "2022-09-13 21:15:47" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000418485" "00417198" "1" "00006" "00006" "2022-09-13 21:20:43" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000418486" "00417199" "1" "00006" "00006" "2022-09-13 21:25:54" "" "" "SEQ;SEQ-NG" "DNA" "" "WES" "0000418487" "00417200" "1" "00006" "00006" "2022-09-13 21:33:53" "" "" "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 = 7 "{{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}}" "0000716800" "0" "50" "1" "151143398" "151143398" "subst" "0" "02327" "TMOD4_000001" "g.151143398G>A" "" "" "" "" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "" "" "VUS" "" "0000878253" "3" "90" "1" "151139474" "151139474" "del" "0" "00006" "SCNM1_000001" "g.151139474del" "" "{PMID:Iturrate 2022:36084634}, {DOI:Iturrate 2022:10.1016/j.ajhg.2022.08.009}" "" "187delC" "" "Germline" "yes" "" "0" "" "" "g.151166998del" "" "pathogenic (recessive)" "" "0000878254" "3" "90" "1" "151139474" "151139474" "del" "0" "00006" "SCNM1_000001" "g.151139474del" "" "{PMID:Iturrate 2022:36084634}, {DOI:Iturrate 2022:10.1016/j.ajhg.2022.08.009}" "" "187delC" "" "Germline" "yes" "" "0" "" "" "g.151166998del" "" "pathogenic (recessive)" "" "0000878255" "3" "70" "1" "151139439" "151139439" "subst" "0" "00006" "SCNM1_000002" "g.151139439C>A" "" "{PMID:Iturrate 2022:36084634}, {DOI:Iturrate 2022:10.1016/j.ajhg.2022.08.009}" "" "" "effect on splicing derived from expression cloning mini-gene splicing assay in RPE1 cells" "Germline" "" "" "0" "" "" "g.151166963C>A" "" "likely pathogenic (recessive)" "" "0000878257" "3" "90" "1" "151139686" "151139687" "ins" "0" "00006" "SCNM1_000003" "g.151139686_151139687ins[[NC_000015.9:g.44813855_44814157];151139670_151139686]" "" "{PMID:Iturrate 2022:36084634}, {DOI:Iturrate 2022:10.1016/j.ajhg.2022.08.009}" "" "301_302insAluYc, 283T>A;284T>A" "" "Germline" "" "" "0" "" "" "" "" "likely pathogenic (recessive)" "" "0000960491" "0" "30" "1" "151134589" "151134589" "dup" "0" "02329" "LYSMD1_000001" "g.151134589dup" "" "" "" "LYSMD1(NM_212551.5):c.181-4dupT" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "likely benign" "" "0000990263" "0" "50" "1" "151143146" "151143146" "subst" "1.22555E-5" "01804" "LYSMD1_000002" "g.151143146G>A" "" "" "" "TMOD4(NM_013353.2):c.871-7C>T (p.?)" "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 SCNM1 ## Count = 7 "{{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}}" "0000716800" "00018528" "50" "2530" "0" "2530" "0" "c.*1837G>A" "r.(=)" "p.(=)" "" "0000878253" "00018528" "90" "187" "0" "187" "0" "c.187del" "r.(?)" "p.(Arg63Valfs*33)" "" "0000878254" "00018528" "90" "187" "0" "187" "0" "c.187del" "r.(?)" "p.(Arg63Valfs*33)" "" "0000878255" "00018528" "70" "152" "0" "152" "0" "c.152C>A" "r.(123_153del)" "p.(he42Tyrfs*8)" "3" "0000878257" "00018528" "90" "301" "0" "302" "0" "c.301_302ins[[NC_000015.9:g.44813855_44814157];285_301]" "r.?" "p.?" "4" "0000960491" "00018528" "30" "-4040" "0" "-4040" "0" "c.-4040dup" "r.(?)" "p.(=)" "" "0000990263" "00018528" "50" "2278" "0" "2278" "0" "c.*1585G>A" "r.(=)" "p.(=)" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 4 "{{screeningid}}" "{{variantid}}" "0000418484" "0000878253" "0000418485" "0000878254" "0000418486" "0000878255" "0000418487" "0000878257"