### LOVD-version 3000-30b ### Full data download ### To import, do not remove or alter this header ### ## Filter: (gene_public = PHF5A) # 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}}" "PHF5A" "PHD finger protein 5A" "22" "q13.2" "unknown" "NC_000022.10" "UD_132463270562" "" "" "" "1" "18000" "84844" "0" "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/PHF5A_codingDNA.html" "1" "" "" "-1" "" "-1" "00001" "2013-05-03 00:00:00" "00006" "2023-08-30 09:57:29" "00000" "2025-11-01 13:22:20" ## 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}}" "00016076" "PHF5A" "PHD finger protein 5A" "001" "NM_032758.3" "" "NP_116147.1" "" "" "" "-51" "1014" "333" "41864708" "41855721" "" "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}}" "05162" "DD" "developmental delay (DD)" "" "" "" "" "" "00006" "2016-05-10 21:15:54" "00006" "2020-05-25 13:52:33" ## Genes_To_Diseases ## Do not remove or alter this header ## ## Count = 0 ## Individuals ## Do not remove or alter this header ## ## Count = 9 "{{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}}" "00424800" "" "" "" "1" "" "03578" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "F" "no" "" "" "0" "" "" "" "Pat1" "00424801" "" "" "" "1" "" "03578" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "M" "no" "" "" "0" "" "" "" "Pat2" "00424827" "" "" "" "1" "" "03578" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "M" "no" "" "" "0" "" "" "" "Pat3" "00424828" "" "" "" "1" "" "03578" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "M" "no" "" "" "0" "" "" "" "Pat4" "00424829" "" "" "" "1" "" "03578" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "F" "no" "" "" "0" "" "" "" "Pat6" "00424913" "" "" "" "1" "" "03578" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "F" "" "" "" "0" "" "" "" "Pat9" "00427965" "" "" "" "1" "" "03578" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "M" "" "" "" "0" "" "" "" "Pat8" "00435027" "" "" "" "1" "" "03578" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "" "no" "? (unknown)" "" "0" "" "" "" "Pat5" "00436161" "" "" "" "1" "" "00006" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "F" "no" "" "" "0" "" "" "" "Pat7" ## Individuals_To_Diseases ## Do not remove or alter this header ## ## Count = 9 "{{individualid}}" "{{diseaseid}}" "00424800" "05162" "00424801" "05162" "00424827" "05162" "00424828" "05162" "00424829" "05162" "00424913" "05162" "00427965" "05162" "00435027" "05162" "00436161" "05162" ## Phenotypes ## Do not remove or alter this header ## ## Note: Only showing Phenotype columns active for Diseases 05162 ## Count = 9 "{{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}}" "0000315995" "05162" "00424800" "03578" "-" "05y10m" "Caesarian section (HP:0011410); Premature birth (HP:0001622); Sacral dimple (HP:0000960); Macrocephaly (HP:0000256); Motor delay (HP:0001270); Speech delay (HP:0000750); High forehead (HP:0000348); Hypertelorism (HP:0000316); Periorbital fullness (HP:0000629)" "" "" "" "" "" "" "" "" "" "0000315996" "05162" "00424801" "03578" "Unknown" "19y" "Intrauterine growth retardation (HP:0001511); Premature birth (HP:0001622); Respiratory failure requiring assisted ventilation (HP:0004887); Hypospadias (HP:0000047); Inguinal hernia (HP:0000023); Sacral dimple (HP:0000960); Small for gestational age (HP:0001518); Microcephaly (HP:0000252); Short stature (HP:0004322); Motor delay (HP:0001270); Speech delay (HP:0000750); Preauricular skin tag (HP:0000384); Deeply set eyes (HP:0000490)" "" "" "" "" "" "" "" "" "" "0000316022" "05162" "00424827" "03578" "Unknown" "07y11m" "Intrauterine growth retardation (HP:0001511); Caesarian section (HP:0011410); Premature birth (HP:0001622); Respiratory failure requiring assisted ventilation (HP:0004887); Hypospadias (HP:0000047); Inguinal hernia (HP:0000023); Motor delay (HP:0001270); Speech delay (HP:0000750); Intellectual disability (HP:0001249); Intellectual disability, mild (HP:0001256); Hypotonia (HP:0001252); Seizure (HP:0001250); Autistic behavior (HP:0000729); Sleep disturbance (HP:0002360); High forehead (HP:0000348); Preauricular skin tag (HP:0000384); Downslanted palpebral fissures (HP:0000494); Deeply set eye (HP:0000490)" "" "" "" "" "" "" "" "" "" "0000316023" "05162" "00424828" "03578" "Unknown" "05y08m" "Caesarian section (HP:0011410); Abnormal aortic arch morphology (HP:0012303); Ventricular septal defect (HP:0001629); Motor delay (HP:0001270); Speech delay (HP:0000750); Postaxial polydactyly (HP:0100259); High forehead (HP:0000348); Preauricular skin tag (HP:0000384); Periorbital fullness (HP:0000629); Deeply set eyes (HP:0000490); Low-set ears (HP:0000369)" "" "" "" "" "" "" "" "" "" "0000316024" "05162" "00424829" "03578" "Unknown" "19y" "Intrauterine growth retardation (HP:0001511); Caesarian section (HP:0011410); Premature birth (HP:0001622); Respiratory failure requiring assisted ventilation (HP:0004887); Motor delay (HP:0001270); Speech delay (HP:0000750); Intellectual disability (HP:0001249); Intellectual disability, mild (HP:0001256); Preauricular skin tag (HP:0000384); Hypertelorism (HP:0000316); Broad toe (HP:0001837); Long fingers (HP:0100807); Low-set ears (HP:0000369); Retrognathia (HP:0000278)" "" "" "" "" "" "" "" "" "" "0000316112" "05162" "00424913" "03578" "Unknown" "06y06m" "Intrauterine growth retardation (HP:0001511); Atrial septal defect (HP:0001631) Small for gestational age (HP:0001518); Microcephaly (HP:0000252); Short stature (HP:0004322); Motor delay (HP:0001270); Speech delay (HP:0000750); Intellectual disability (HP:0001249); Hypotonia (HP:0001252); Low-set ears (HP:0000369)" "" "" "" "" "" "" "" "" "" "0000318911" "05162" "00427965" "03578" "Unknown" "24y" "Hypospadias (HP:0000047); Atrial septal defect (HP:0001631); Inguinal hernia (HP:0000023); Sacral dimple (HP:0000960); Short stature (HP:0004322); Motor delay (HP:0001270); Speech delay (HP:0000750); Hypotonia (HP:0001252); Broad toes (HP:0001837); Short distal phalanx of hallux (HP:0010103); Small nails (HP:0001792) and nail dysplasia (HP:0002164); Downslanted palpebral fissures (HP:0000494)" "" "" "" "" "" "" "" "" "" "0000325269" "05162" "00435027" "03578" "Unknown" "11y" "Intrauterine growth retardation (HP:0001511); Small for gestational age (HP:0001518); Short stature (HP:0004322); Motor delay (HP:0001270); Speech delay (HP:0000750); Intellectual disability (HP:0001249); Intellectual disability, mild (HP:0001256); Hypotonia (HP:0001252); Talipes equinovarus (HP:0001762); Long fingers (HP:0100807); Broad toes (HP:0001837); nail dysplasia (HP:0002164);Preauricular skin tag (HP:0000384); Periorbital fullness (HP:0000629); Hypertelorism (HP:0000316);Hypertelorism (HP:0000316); Low-set ears (HP:0000369)" "" "" "" "" "" "" "" "" "" "0000326342" "05162" "00436161" "00006" "Isolated (sporadic)" "17y" "intrauterine growth retardation (HP:0001511); Caesarian section (HP:0011410); no premature birth (-HP:0001622); no respiratory failure requiring assisted ventilation (-HP:0004887); no abnormal aortic arch morphology (-HP:0012303); no atrial septal defect (-HP:0001631); no ventricular septal defect (-HP:0001629); no inguinal hernia (-HP:0000023); no sacral dimple (-HP:0000960); small for gestational age (HP:0001518); no microcephaly (-HP:0000252); no macrocephaly (-HP:0000256); short stature (HP:0004322); motor delay (HP:0001270); speech delay (HP:0000750); mild intellectual disability (HP:0001256); no hypotonia (-HP:0001252); no seizure (-HP:0001250); no autistic behavior (-HP:0000729); no sleep disturbance (-HP:0002360); no talipes equinovarus (-HP:0001762); no postaxial polydactyly (-HP:0100259); long fingers (HP:0100807); no broad toes (-HP:0001837); no short distal phalanx of hallux (-HP:0010103); no small nails (-HP:0001792); no nail dysplasia (-HP:0002164); high forehead (HP:0000348); no preauricular skin tag (-HP:0000384); periorbital fullness (HP:0000629); deeply set eyes (HP:0000490); no hypertelorism (-HP:0000316); no downslanted palpebral fissures (-HP:0000494); no low-set ears (-HP:0000369); no retrognathia (-HP:0000278)" "" "" "" "" "" "" "" "" "" ## Screenings ## Do not remove or alter this header ## ## Count = 9 "{{id}}" "{{individualid}}" "{{variants_found}}" "{{owned_by}}" "{{created_by}}" "{{created_date}}" "{{edited_by}}" "{{edited_date}}" "{{Screening/Technique}}" "{{Screening/Template}}" "{{Screening/Tissue}}" "{{Screening/Remarks}}" "0000426113" "00424800" "1" "03578" "03578" "2022-11-22 14:21:26" "" "" "SEQ-NG" "DNA" "blood" "WES" "0000426114" "00424801" "1" "03578" "03578" "2022-11-22 14:28:14" "" "" "SEQ-NG" "DNA" "blood" "WES" "0000426140" "00424827" "1" "03578" "03578" "2022-11-22 14:53:39" "" "" "SEQ-NG" "DNA" "blood" "WES" "0000426141" "00424828" "1" "03578" "03578" "2022-11-22 15:02:43" "" "" "SEQ-NG" "DNA" "blood" "WES" "0000426142" "00424829" "1" "03578" "03578" "2022-11-22 15:09:03" "" "" "SEQ-NG" "DNA" "blood" "WES" "0000426232" "00424913" "1" "03578" "03578" "2022-11-23 10:03:30" "03578" "2022-11-23 11:23:40" "SEQ-NG" "DNA" "blood" "WGS" "0000429378" "00427965" "1" "03578" "03578" "2022-12-19 11:29:30" "" "" "SEQ-NG" "DNA" "blood" "WES" "0000436500" "00435027" "1" "03578" "03578" "2023-04-20 07:51:04" "" "" "SEQ-NG" "DNA" "" "WES" "0000437644" "00436161" "1" "00006" "00006" "2023-08-30 10:14:17" "" "" "SEQ-NG" "DNA" "" "WES" ## Screenings_To_Genes ## Do not remove or alter this header ## ## Count = 8 "{{screeningid}}" "{{geneid}}" "0000426113" "PHF5A" "0000426114" "PHF5A" "0000426140" "PHF5A" "0000426141" "PHF5A" "0000426142" "PHF5A" "0000426232" "PHF5A" "0000429378" "PHF5A" "0000436500" "PHF5A" ## 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 = 12 "{{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}}" "0000305532" "0" "50" "22" "41864647" "41864647" "subst" "0" "01943" "PHF5A_000001" "g.41864647T>C" "" "" "" "PHF5A(NM_032758.4):c.11A>G (p.H4R)" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.41468643T>C" "" "VUS" "" "0000572165" "0" "50" "22" "41864657" "41864657" "subst" "0" "02327" "ACO2_000032" "g.41864657T>A" "" "" "" "" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "0" "" "" "g.41468653T>A" "" "VUS" "" "0000902940" "0" "70" "22" "41864656" "41864656" "subst" "0" "03578" "PHF5A_000002" "g.41864656A>G" "" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "" "" "De novo" "yes" "" "0" "" "" "g.41468652A>G" "" "likely pathogenic (dominant)" "ACMG" "0000902942" "0" "70" "22" "41864138" "41864139" "del" "0" "03578" "PHF5A_000003" "g.41864138_41864139del" "" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "" "" "De novo" "yes" "" "0" "" "" "g.41468134_41468135del" "" "likely pathogenic" "ACMG" "0000902968" "0" "70" "22" "41864138" "41864139" "del" "0" "03578" "PHF5A_000003" "g.41864138_41864139del" "" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "" "" "De novo" "yes" "" "0" "" "" "g.41468134_41468135del" "" "likely pathogenic" "ACMG" "0000902970" "0" "70" "22" "41864134" "41864134" "subst" "0" "03578" "PHF5A_000004" "g.41864134C>A" "" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "" "" "De novo" "yes" "" "0" "" "" "g.41468130C>A" "" "likely pathogenic" "ACMG" "0000902971" "0" "70" "22" "41856462" "41856462" "dup" "0" "03578" "PHF5A_000005" "g.41856462dup" "" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "" "" "De novo" "yes" "" "0" "" "" "g.41460458dup" "" "likely pathogenic" "ACMG" "0000903162" "0" "70" "22" "41863510" "41863510" "subst" "0" "03578" "PHF5A_000006" "g.41863510C>T" "" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "" "" "De novo" "yes" "" "0" "" "" "g.41467506C>T" "" "likely pathogenic" "ACMG" "0000908850" "0" "70" "22" "41864614" "41864614" "subst" "0" "03578" "PHF5A_000007" "g.41864614G>A" "" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "" "" "De novo" "" "" "0" "" "" "g.41468610G>A" "" "VUS" "ACMG" "0000927485" "0" "90" "22" "41863451" "41863451" "subst" "0" "03578" "PHF5A_000008" "g.41863451C>T" "" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "" "" "De novo" "" "" "0" "" "" "g.41467447C>T" "" "likely pathogenic" "ACMG" "0000932987" "0" "90" "22" "41864647" "41864647" "subst" "0" "00006" "PHF5A_000001" "g.41864647T>C" "" "{PMID:Harms 2023:37422718}, {DOI:Harms 2023:10.1016/j.gim.2023.100927}" "" "" "" "De novo" "" "" "0" "" "" "g.41468643T>C" "" "likely pathogenic (dominant)" "" "0001057193" "0" "70" "22" "41863531" "41863531" "del" "0" "01804" "ACO2_000180" "g.41863531del" "" "" "" "PHF5A(NM_032758.4):c.164del (p.(Gln55Argfs*5))" "VKGL data sharing initiative Nederland" "CLASSIFICATION record" "" "" "" "" "" "" "" "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 PHF5A ## Count = 12 "{{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}}" "0000305532" "00016076" "50" "11" "0" "11" "0" "c.11A>G" "r.(?)" "p.(His4Arg)" "" "0000572165" "00016076" "50" "1" "0" "1" "0" "c.1A>T" "r.(?)" "p.(Met1?)" "" "0000902940" "00016076" "70" "2" "0" "2" "0" "c.2T>C" "r.2u>c" "p.?" "1" "0000902942" "00016076" "70" "69" "0" "70" "0" "c.69_70del" "r.(69_70del)" "p.(Cys23*)" "2" "0000902968" "00016076" "70" "69" "0" "70" "0" "c.69_70del" "r.(69_70del)" "p.(Cys23*)" "2" "0000902970" "00016076" "70" "70" "0" "70" "0" "c.70G>T" "r.(70g>u)" "p.(Glu24*)" "2" "0000902971" "00016076" "70" "276" "0" "276" "0" "c.276dup" "r.(276dup)" "p.(Ser93Glufs*3)" "4" "0000903162" "00016076" "70" "185" "0" "185" "0" "c.185G>A" "r.(185g>a)" "p.(Gly62Glu)" "3" "0000908850" "00016076" "70" "44" "0" "44" "0" "c.44C>T" "r.(?)" "p.(Ala15Val)" "1" "0000927485" "00016076" "90" "243" "1" "243" "1" "c.243+1G>A" "r.spl?" "p.?" "" "0000932987" "00016076" "90" "11" "0" "11" "0" "c.11A>G" "r.(?)" "p.(His4Arg)" "" "0001057193" "00016076" "70" "164" "0" "164" "0" "c.164del" "r.(?)" "p.(Gln55Argfs*5)" "" ## Screenings_To_Variants ## Do not remove or alter this header ## ## Count = 9 "{{screeningid}}" "{{variantid}}" "0000426113" "0000902940" "0000426114" "0000902942" "0000426140" "0000902968" "0000426141" "0000902970" "0000426142" "0000902971" "0000426232" "0000903162" "0000429378" "0000908850" "0000436500" "0000927485" "0000437644" "0000932987"