MSeqDR Mitochondrial Disease Portal


 
*:HP: HPO terms, UMDF: 1= Disease, ND: NAMDC terms.
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Abnormalities, Multiple (D000015)
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Intellectual Disability (D008607)
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Phosphorus Metabolism Disorders (D010760)
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Hyperphosphatasia with Mental Retardation (C565495)

       Child Nodes:
........expandHYPERPHOSPHATASIA WITH MENTAL RETARDATION SYNDROME 3 (OMIM:614207)



 Sister Nodes: 
..expandHyperphosphatasia with Mental Retardation (C565495) Child2
..expandHyperphosphatemia (D054559) Child3
..expandHypophosphatemia (D017674) Child17
   

Human Disease MESH is developed by UMLS.
Further data from MedGen, OMIM,ClinVar, CTD
Term ID:5940
Name:Hyperphosphatasia with Mental Retardation
Definition:
Alternative IDs:OMIM:239300|OMIM:614749|OMIM:615716|OMIM:616025|OMIM:616809
ParentIDs:MESH:D000015|MESH:D008607|MESH:D010760
TreeNumbers:C10.597.606.360/C565495 |C16.131.077/C565495 |C18.452.750/C565495 |C23.888.592.604.646/C565495 |F03.625.539/C565495
Synonyms:GLYCOSYLPHOSPHATIDYLINOSITOL BIOSYNTHESIS DEFECT 10 |GLYCOSYLPHOSPHATIDYLINOSITOL BIOSYNTHESIS DEFECT 11 |GLYCOSYLPHOSPHATIDYLINOSITOL BIOSYNTHESIS DEFECT 12 |GLYCOSYLPHOSPHATIDYLINOSITOL BIOSYNTHESIS DEFECT 2 |GLYCOSYLPHOSPHATIDYLINOSITOL BIOSYNTHESIS DEFEC
Slim Mappings:Congenital abnormality|Mental disorder|Metabolic disease|Nervous system disease|Signs and symptoms
Reference: MedGen: C565495
MeSH: C565495
OMIM: 239300;
MSeqDR LSDB:  
Genes: PGAP3; PIGO; PIGV; PIGW;
Phenotypes
1 HP:0000007Autosomal recessive inheritance
2 HP:0001090Abnormally large globeHP:0040282
3 HP:0001344Absent speechHP:0040281
4 HP:0002251Aganglionic megacolonHP:0040284
5 HP:0001545Anteriorly placed anusHP:0040284
6 HP:0000455Broad nasal tipHP:0040284
7 HP:0000175Cleft palateHP:0040283
8 HP:0000204Cleft upper lipHP:0040284
9 HP:0002019ConstipationHP:0040284
10 HP:0001216Delayed ossification of carpal bonesHP:0040284
11 HP:0002714Downturned corners of mouthHP:0040284
12 HP:0003155Elevated alkaline phosphataseHP:0040284
13 HP:0001290Generalized hypotonia
14 HP:0002553Highly arched eyebrow
15 HP:0000238HydrocephalusHP:0040284
16 HP:0000316HypertelorismHP:0040284
17 HP:0001249Intellectual disabilityHP:0040284
18 HP:0010864Intellectual disability, severe
19 HP:0000637Long palpebral fissureHP:0040282
20 HP:0000272Malar flattening
21 HP:0000303Mandibular prognathia
22 HP:0011800Midface retrusion
23 HP:0001252Muscular hypotonia
NAMDC:  Hypotonia
HP:0040284 Infantile onset
24 HP:0001357Plagiocephaly
25 HP:0000358Posteriorly rotated earsHP:0040282
26 HP:0001250Seizures
NAMDC:  Seizures
HP:0040284
27 HP:0000407Sensorineural hearing impairment
NAMDC:  Sensorineural hearing loss
HP:0040284
28 HP:0009882Short distal phalanx of fingerHP:0040284
29 HP:0000322Short philtrum
30 HP:0001831Short toeHP:0040283
31 HP:0001792Small nailHP:0040282
32 HP:0001182Tapered finger
33 HP:0010804Tented upper lip vermilion
34 HP:0000219Thin upper lip vermilionHP:0040282
35 HP:0000582Upslanted palpebral fissureHP:0040282
36 HP:0000431Wide nasal bridgeHP:0040284
Disease Causing ClinVar Variants
Variation_NameGeneIDGeneSymbolClinicalSignificancedbSNPRCVaccessionTestedInGTRPhenotypeIDsChromosomeStartStopHGVS_cHGVS_pHGVS_gOtherIDsDisease_ClinVar
NM_004855.5(PIGB):c.1220A>G (p.His407Arg)9488PIGBUncertain significancers1566960044RCV000680066|RCV000850266; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:247262|MONDO:MONDO:0032822,MedGen:C5231418,OMIM:618580155564299355642993AG15:g.55642993A>GOMIM:604122.0005
NM_001127178.3(PIGG):c.2005C>T (p.Arg669Cys)54872PIGGConflicting interpretations of pathogenicityrs372392424RCV000210937|RCV000856757; NMONDO:MONDO:0014832,MedGen:C4310794,OMIM:616917, Orphanet:488635|MONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:2472624517638517638CT4:g.517638C>TClinGen:CA2793501,UniProtKB:Q5H8A4#VAR_076775,OMIM:616918.0002C4310794 616917 Mental retardation, autosomal recessive 53;
NM_032634.4(PIGO):c.2397A>C (p.Gln799His)84720PIGOPathogenicrs1587162510RCV000856762; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726293509148735091487TG9:g.35091487T>G-
NM_017837.3(PIGV):c.-338A>C55650PIGVBenignrs113400508RCV000276263; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212711447927114479AC1:g.27114479A>CClinGen:CA10610887C1855923 Hyperphosphatasia-intellectual disability syndrome;
NM_017837.3(PIGV):c.-333C>T55650PIGVBenignrs118069986RCV000326362; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212711448427114484CT1:g.27114484C>TClinGen:CA10610048C1855923 Hyperphosphatasia-intellectual disability syndrome;
NM_017837.3(PIGV):c.-323C>T55650PIGVUncertain significancers771484813RCV000362433; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212711449427114494CT1:g.27114494C>TClinGen:CA10610889C1855923 Hyperphosphatasia-intellectual disability syndrome;
NM_017837.4(PIGV):c.-184G>T55650PIGVUncertain significance-1RCV001101542; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212711463327114633GT1:g.27114633G>T-
NM_017837.4(PIGV):c.-166G>A55650PIGVUncertain significance-1RCV001101543; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212711465127114651GA1:g.27114651G>A-
NM_017837.4(PIGV):c.-68G>A55650PIGVUncertain significance-1RCV001096101; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212711474927114749GA1:g.27114749G>A-
NM_017837.3(PIGV):c.-57-6G>A55650PIGVUncertain significancers931609061RCV000272689; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212711724427117244GA1:g.27117244G>AClinGen:CA10610961C1855923 Hyperphosphatasia-intellectual disability syndrome;
NM_017837.3(PIGV):c.55C>T (p.Arg19Cys)55650PIGVLikely pathogenicrs759988046RCV000660523; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212711736127117361CT1:g.27117361C>T-CN030519 239300 Hyperphosphatasia with mental retardation syndrome 1;
NM_017837.4(PIGV):c.78+4A>G55650PIGVUncertain significance-1RCV001096102; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212711738827117388AG1:g.27117388A>G-
NM_017837.3(PIGV):c.101C>T (p.Pro34Leu)55650PIGVBenignrs139246652RCV000327702|RCV000427983|RCV000966354; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:247262|MedGen:CN169374|MedGen:CN51720212712062627120626CT1:g.27120626C>TClinGen:CA707995C1855923 Hyperphosphatasia-intellectual disability syndrome;
NM_017837.3(PIGV):c.115G>A (p.Glu39Lys)55650PIGVUncertain significancers369275802RCV000521292|RCV000765106; NMedGen:CN169374|MONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712064027120640GA1:g.27120640G>AClinGen:CA707998CN169374 not specified;
NM_017837.3(PIGV):c.134G>A (p.Arg45His)55650PIGVUncertain significancers148135928RCV000726136|RCV000768044; NMedGen:CN517202|MONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712065927120659GA1:g.27120659G>AClinGen:CA708002CN169374 not specified;
NM_017837.4(PIGV):c.223G>A (p.Ala75Thr)55650PIGVUncertain significance-1RCV001096103; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712074827120748GA1:g.27120748G>A-
NM_017837.4(PIGV):c.265C>T (p.Pro89Ser)55650PIGVUncertain significance-1RCV001096104; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712079027120790CT1:g.27120790C>T-
NM_017837.4(PIGV):c.312C>G (p.Pro104=)55650PIGVUncertain significance-1RCV001096105; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712083727120837CG1:g.27120837C>G-
NM_017837.3(PIGV):c.348_349delinsAG (p.Ile117Val)55650PIGVUncertain significancers886044116RCV000313858|RCV000726297|RCV000765107; NMedGen:CN169374|MedGen:CN517202|MONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712087327120874GAAGNC_000001.10:g.27120873_27120874delinsAGClinGen:CA10606367CN169374 not specified;
NM_017837.3(PIGV):c.348G>A (p.Leu116=)55650PIGVConflicting interpretations of pathogenicityrs148662665RCV000376742|RCV000455608|RCV000512822; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:247262|MedGen:CN169374|MedGen:CN51720212712087327120873GA1:g.27120873G>AClinGen:CA708043C1855923 Hyperphosphatasia-intellectual disability syndrome;
NM_017837.3(PIGV):c.349A>G (p.Ile117Val)55650PIGVConflicting interpretations of pathogenicityrs142192097RCV000286962|RCV000455981|RCV000514626; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:247262|MedGen:CN169374|MedGen:CN51720212712087427120874AG1:g.27120874A>GClinGen:CA708044
NM_017837.3(PIGV):c.467G>A (p.Cys156Tyr)55650PIGVLikely pathogenicrs387907023RCV000023806|RCV000413902; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:247262|MedGen:CN51720212712099227120992GA1:g.27120992G>AClinGen:CA129484,OMIM:610274.0005CN030519 239300 Hyperphosphatasia with mental retardation syndrome 1;
NM_017837.4(PIGV):c.473G>A (p.Ser158Asn)55650PIGVLikely benignrs201332799RCV000908864|RCV001097856; NMedGen:CN517202|MONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712099827120998GA1:g.27120998G>A-
NM_017837.3(PIGV):c.494C>A (p.Ala165Glu)55650PIGVPathogenicrs376328153RCV000122740; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712101927121019CA1:g.27121019C>AClinGen:CA163121,OMIM:610274.0006CN030519 239300 Hyperphosphatasia with mental retardation syndrome 1;
NM_017837.3(PIGV):c.531A>T (p.Thr177=)55650PIGVUncertain significancers1057515474RCV000323165; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712105627121056AT1:g.27121056A>TClinGen:CA10610890
NM_017837.4(PIGV):c.607C>T (p.Arg203Cys)55650PIGVPathogenic/Likely pathogenic-1RCV001090918|RCV001262427; NMedGen:CN517202|MONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712113227121132CT1:g.27121132C>T-
NM_017837.3(PIGV):c.614A>G (p.Asn205Ser)55650PIGVConflicting interpretations of pathogenicityrs766452597RCV000482776|RCV001097857|RCV001267017; NMedGen:CN517202|MONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:247262|MeSH:D030342,MedGen:C095012312712113927121139AG1:g.27121139A>GClinGen:CA708081CN517202 not provided;
NM_017837.3(PIGV):c.615C>T (p.Asn205=)55650PIGVBenign/Likely benignrs34512715RCV000428348|RCV000513788|RCV001097858; NMedGen:CN169374|MedGen:CN517202|MONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712114027121140CT1:g.27121140C>TClinGen:CA708082CN517202 not provided;
NM_017837.3(PIGV):c.728T>C (p.Leu243Pro)55650PIGVUncertain significancers771841963RCV000768045; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712125327121253TC1:g.27121253T>C-
NM_017837.4(PIGV):c.732G>A (p.Ser244=)55650PIGVUncertain significance-1RCV001097859; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712125727121257GA1:g.27121257G>A-
NM_017837.3(PIGV):c.766C>A (p.Gln256Lys)55650PIGVPathogenicrs267606952RCV000001349; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712129127121291CA1:g.27121291C>AUniProtKB:Q9NUD9#VAR_064190,OMIM:610274.0003,ClinGen:CA114904CN030519 239300 Hyperphosphatasia with mental retardation syndrome 1;
NM_017837.3(PIGV):c.808C>T (p.Arg270Cys)55650PIGVUncertain significancers374158705RCV000373188; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712133327121333CT1:g.27121333C>TClinGen:CA708120
NM_017837.3(PIGV):c.809G>A (p.Arg270His)55650PIGVConflicting interpretations of pathogenicityrs149379900RCV000600573|RCV001097860; NMedGen:CN169374|MONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712133427121334GA1:g.27121334G>AClinGen:CA708121CN169374 not specified;
NM_017837.3(PIGV):c.851G>A (p.Gly284Asp)55650PIGVUncertain significancers557206710RCV000278822; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712137627121376GA1:g.27121376G>AClinGen:CA708129
NM_017837.3(PIGV):c.879G>A (p.Pro293=)55650PIGVConflicting interpretations of pathogenicityrs147229452RCV000430252|RCV001099655; NMedGen:CN169374|MONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712140427121404GA1:g.27121404G>AClinGen:CA708135CN169374 not specified;
NM_017837.4(PIGV):c.968A>G (p.Lys323Arg)55650PIGVUncertain significance-1RCV001099656; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712149327121493AG1:g.27121493A>G-
NM_017837.4(PIGV):c.980A>G (p.Asn327Ser)55650PIGVUncertain significance-1RCV001099657; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712150527121505AG1:g.27121505A>G-
NM_017837.3(PIGV):c.1008A>G (p.Ile336Met)55650PIGVUncertain significancers1057515437RCV000338501; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712153327121533AG1:g.27121533A>GClinGen:CA10609835
NM_017837.3(PIGV):c.1022C>A (p.Ala341Glu)55650PIGVPathogenic/Likely pathogenicrs139073416RCV000001347|RCV000190698|RCV000396582|RCV000613584; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:247262|MeSH:D030342,MedGen:C0950123|MedGen:CN517202|MONDO:MONDO:0016596,MedGen:C1855923,OMIM:PS239300, Orphanet:24726212712154727121547CA1:g.27121547C>AClinGen:CA114900,UniProtKB:Q9NUD9#VAR_064191,OMIM:610274.0001CN030519 239300 Hyperphosphatasia with mental retardation syndrome 1;
NM_017837.3(PIGV):c.1022C>T (p.Ala341Val)55650PIGVPathogenicrs139073416RCV000001350; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712154727121547CT1:g.27121547C>TClinGen:CA114906,UniProtKB:Q9NUD9#VAR_064192,OMIM:610274.0004CN030519 239300 Hyperphosphatasia with mental retardation syndrome 1;
NM_017837.3(PIGV):c.1147G>A (p.Val383Met)55650PIGVUncertain significancers765449173RCV000521023|RCV001099658; NMedGen:CN517202|MONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712167227121672GA1:g.27121672G>AClinGen:CA708171CN169374 not specified;
NM_017837.3(PIGV):c.1154A>C (p.His385Pro)55650PIGVPathogenicrs267606951RCV000001348; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712167927121679AC1:g.27121679A>CClinGen:CA114902,UniProtKB:Q9NUD9#VAR_064193,OMIM:610274.0002CN030519 239300 Hyperphosphatasia with mental retardation syndrome 1;
NM_017837.3(PIGV):c.1213T>A (p.Phe405Ile)55650PIGVUncertain significancers1057515509RCV000391703; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712406627124066TA1:g.27124066T>AClinGen:CA10610051
NM_017837.3(PIGV):c.1277C>T (p.Pro426Leu)55650PIGVConflicting interpretations of pathogenicityrs146969255RCV000178312|RCV000294158|RCV000724080; NMedGen:CN169374|MONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:247262|MedGen:CN51720212712413027124130CT1:g.27124130C>TClinGen:CA245378C1855923 Hyperphosphatasia-intellectual disability syndrome;
NM_017837.3(PIGV):c.1369C>T (p.Leu457Phe)55650PIGVConflicting interpretations of pathogenicityrs143676075RCV000490215|RCV000765108|RCV000983824; NMedGen:CN169374|MONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:247262|MedGen:CN51720212712422227124222CT1:g.27124222C>TClinGen:CA708215CN169374 not specified;
NM_017837.3(PIGV):c.1464C>T (p.Asn488=)55650PIGVUncertain significancers973687848RCV000349117; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712431727124317CT1:g.27124317C>TClinGen:CA10610891
NM_017837.4(PIGV):c.1467C>G (p.Phe489Leu)55650PIGVUncertain significance-1RCV001101648; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712432027124320CG1:g.27124320C>G-
NM_017837.3(PIGV):c.1477A>G (p.Thr493Ala)55650PIGVUncertain significancers1057515548RCV000403426; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712433027124330AG1:g.27124330A>GClinGen:CA10609838
NM_017837.3(PIGV):c.*110T>C55650PIGVUncertain significancers1057515439RCV000313418; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712444527124445TC1:g.27124445T>CClinGen:CA10610897
NM_017837.4(PIGV):c.*114C>A55650PIGVUncertain significance-1RCV001101649; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712444927124449CA1:g.27124449C>A-
NM_017837.3(PIGV):c.*149G>A55650PIGVBenignrs3754360RCV000363388; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712448427124484GA1:g.27124484G>AClinGen:CA10610898
NM_017837.4(PIGV):c.*167G>A55650PIGVBenign-1RCV001101650; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712450227124502GA1:g.27124502G>A-
NM_017837.3(PIGV):c.*186G>T55650PIGVUncertain significancers1057515440RCV000405349; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712452127124521GT1:g.27124521G>TClinGen:CA10610969
NM_017837.3(PIGV):c.*210A>G55650PIGVBenignrs57189461RCV000309879; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712454527124545AG1:g.27124545A>GClinGen:CA10610052
NM_017837.3(PIGV):c.*367A>G55650PIGVUncertain significancers1057515475RCV000364447; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712470227124702AG1:g.27124702A>GClinGen:CA10610899
NM_017837.3(PIGV):c.*385A>T55650PIGVUncertain significancers754912311RCV000265213; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712472027124720AT1:g.27124720A>TClinGen:CA10609839
NM_017837.3(PIGV):c.*441C>T55650PIGVUncertain significancers777566769RCV000321316; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712477627124776CT1:g.27124776C>TClinGen:CA10610053
NM_017837.3(PIGV):c.*453A>T55650PIGVUncertain significancers1057515441RCV000361959; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712478827124788AT1:g.27124788A>TClinGen:CA10610902
NM_017837.4(PIGV):c.*456C>T55650PIGVUncertain significance-1RCV001096210; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712479127124791CT1:g.27124791C>T-
NM_017837.4(PIGV):c.*473T>G55650PIGVUncertain significance-1RCV001096211; NMONDO:MONDO:0009398,MedGen:C4551502,OMIM:239300, Orphanet:24726212712480827124808TG1:g.27124808T>G-
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