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RGD DISEASE ONTOLOGY - ANNOTATIONS

RGD uses the Human Disease Ontology (DO, https://disease-ontology.org/) for disease curation across species. RGD automatically downloads each new release of the ontology on a monthly basis. Some additional terms which are required for RGD's curation purposes but are not currently covered in the official version of DO have been added. As corresponding terms are added to DO, these custom terms are retired and the DO terms substituted in existing annotations and subsequently used for curation.

Term:Sex Chromosome Disorders
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Accession:DOID:9004151 term browser browse the term
Definition:Clinical conditions caused by an abnormal sex chromosome constitution (SEX CHROMOSOME ABERRATIONS), in which there is extra or missing sex chromosome material (either a whole chromosome or a chromosome segment).
Synonyms:exact_synonym: Sex Chromosome Abnormality Disorders;   Sex Chromosome Disorder
 primary_id: MESH:D025064;   RDO:0000368
For additional species annotation, visit the Alliance of Genome Resources.


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fragile X syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Adgb androglobin ISO ClinVar Annotator: match by term: Fragile X syndrome ClinVar NCBI chr 1:4,445,039...4,588,507
Ensembl chr 1:4,445,027...4,560,789
JBrowse link
G Aff2 AF4/FMR2 family, member 2 ISO ClinVar Annotator: match by term: FRAXE MENTAL RETARDATION SYNDROME
ClinVar Annotator: match by OMIM:309548
OMIM
ClinVar
PMID:18414213 PMID:21739600 PMID:22773736 PMID:23562910 PMID:25741868 PMID:28492532 NCBI chr  X:153,539,951...154,051,022
Ensembl chr  X:153,539,668...154,051,181
JBrowse link
G App amyloid beta precursor protein ISO CTD Direct Evidence: therapeutic CTD PMID:22046307 NCBI chr11:24,425,013...24,641,872
Ensembl chr11:24,425,005...24,641,858
JBrowse link
G Cyfip1 cytoplasmic FMR1 interacting protein 1 ISO RGD PMID:22900020 RGD:11558008 NCBI chr 1:114,258,773...114,347,138
Ensembl chr 1:114,258,719...114,347,137
JBrowse link
G Ercc6 ERCC excision repair 6, chromatin remodeling factor ISO RGD PMID:24352881 RGD:10401097 NCBI chr16:8,734,028...8,804,610
Ensembl chr16:8,734,035...8,804,610
JBrowse link
G Fmr1 FMRP translational regulator 1 ISO
IMP
DNA:trinucleotide expansion
ClinVar Annotator: match by term: X-linked mental retardation and macroorchidism
ClinVar Annotator: match by term: Fragile X syndrome
compared to SD control;DNA:deletion:intron 7, exon 8:
CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by null
ClinVar Annotator: match by OMIM:300624
ClinVar
CTD
OMIM
PMID:7530551 PMID:7633450 PMID:7670500 PMID:8156595 PMID:8490650 PMID:9659908 PMID:15028757 PMID:15805463 PMID:16043816 PMID:16510718 PMID:17065172 PMID:18664458 PMID:18835858 PMID:20300527 PMID:21267007 PMID:22043169 PMID:25171808 PMID:25741868 PMID:28616095, PMID:1675488, PMID:30877790, PMID:27465362, PMID:28894415, PMID:24713347, PMID:12032354 RGD:1601178, RGD:38548928, RGD:38548926, RGD:38501107, RGD:11566052, RGD:11566028 NCBI chr  X:154,684,924...154,722,369
Ensembl chr  X:154,684,935...154,722,314
JBrowse link
G Fmr1em1Mzhe FMRP translational regulator 1; CRISPR/Cas9 induced mutant1, Mzhe IMP RGD PMID:28894415 RGD:38501107
G Fmr1em1Sage FMRP translational regulator 1; zinc finger nuclease induced mutant 1, Sigma Advanced Genetic Engineering Labs IMP DNA:deletion:intron 7, exon 8:
compared to SD control;DNA:deletion:intron 7, exon 8:
RGD PMID:27465362, PMID:30877790 RGD:38548926, RGD:38548928
G Grm1 glutamate metabotropic receptor 1 ISO ClinVar Annotator: match by term: Fragile X syndrome ClinVar NCBI chr 1:4,753,141...5,165,859
Ensembl chr 1:4,753,144...5,165,859
JBrowse link
G Mmp9 matrix metallopeptidase 9 treatment ISO protein:increased expression:brain RGD PMID:25466251, PMID:26850918 RGD:13204755, RGD:11572344 NCBI chr 3:161,413,410...161,421,473
Ensembl chr 3:161,413,298...161,421,520
JBrowse link
G Nrxn3 neurexin 3 ISO mRNA:decreased expression:hippocampus,somatosendory cortex RGD PMID:26235839 RGD:11554325 NCBI chr 6:112,133,204...114,069,589
Ensembl chr 6:112,133,204...114,067,564
JBrowse link
G Rab32 RAB32, member RAS oncogene family ISO ClinVar Annotator: match by term: Fragile X syndrome ClinVar NCBI chr 1:4,638,663...4,653,220
Ensembl chr 1:4,637,491...4,653,210
JBrowse link
G Serpina1 serpin family A member 1 ISO ClinVar Annotator: match by term: FRAXE MENTAL RETARDATION SYNDROME ClinVar PMID:1608473 PMID:1889260 PMID:2339709 PMID:2575668 PMID:2696185 PMID:2700304 PMID:2904702 PMID:2989709 PMID:3264419 PMID:3484754 PMID:3500183 PMID:3537008 PMID:3875547 PMID:6306478 PMID:7045697 PMID:7227484 PMID:8970361 PMID:9041988 PMID:9195389 PMID:9569237 PMID:12034572 PMID:14522813 PMID:15115878 PMID:15454649 PMID:15978931 PMID:17964515 PMID:18294358 PMID:18340647 PMID:18414213 PMID:18515255 PMID:18682522 PMID:19083091 PMID:19398551 PMID:19444872 PMID:19738092 PMID:20301692 PMID:20981092 PMID:21067581 PMID:21228398 PMID:21637600 PMID:21960536 PMID:22426792 PMID:22735536 PMID:22912729 PMID:22933512 PMID:22971141 PMID:22975760 PMID:23632999 PMID:23837941 PMID:23858502 PMID:24033266 PMID:24055113 PMID:24082139 PMID:24328305 PMID:24428606 PMID:24518491 PMID:25181470 PMID:25741868 PMID:26243289 PMID:26304913 PMID:26310624 PMID:26672964 PMID:26831755 PMID:26987331 PMID:28492532 NCBI chr 6:127,610,241...127,632,265
Ensembl chr 6:127,610,243...127,632,265
JBrowse link
fragile X-associated tremor/ataxia syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Fmr1 FMRP translational regulator 1 ISO human gene in a mouse model
CTD Direct Evidence: marker/mechanism
OMIM
CTD
PMID:27385396, PMID:15876460 RGD:12050151 NCBI chr  X:154,684,924...154,722,369
Ensembl chr  X:154,684,935...154,722,314
JBrowse link
G Sod1 superoxide dismutase 1 ISO mRNA:increased expression:prefrontal cortex, brain stem (mouse) RGD PMID:24418349 RGD:8655858 NCBI chr11:30,363,282...30,368,858
Ensembl chr11:30,363,280...30,368,862
JBrowse link
Joubert syndrome with orofaciodigital defect term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cplane1 ciliogenesis and planar polarity effector 1 ISO ClinVar Annotator: match by term: Orofaciodigital syndrome 6
ClinVar Annotator: match by term: Orofaciodigital syndrome VI
ClinVar
OMIM
PMID:9536098 PMID:17576681 PMID:18414213 PMID:22425360 PMID:23012439 PMID:23523602 PMID:24091540 PMID:24178751 PMID:25407461 PMID:25741868 PMID:25846457 PMID:25920555 PMID:26092869 PMID:27081551 PMID:27434533 PMID:28125082 PMID:28289185 PMID:28431631 PMID:28454995 PMID:28492532 PMID:28976722 PMID:29321670 PMID:29605658 NCBI chr 2:57,274,175...57,350,003
NCBI chr 2:57,444,373...57,472,465
Ensembl chr 2:57,276,919...57,348,481
JBrowse link
Juberg Hayward Syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Esco2 establishment of sister chromatid cohesion N-acetyltransferase 2 ISO ClinVar Annotator: match by term: Juberg-Hayward syndrome OMIM
ClinVar
PMID:32255174 PMID:32977150 NCBI chr15:42,500,929...42,519,019
Ensembl chr15:42,500,929...42,518,855
JBrowse link
G Flna filamin A ISO ClinVar Annotator: match by term: Cranio-oro-digital syndrome ClinVar PMID:10982489 PMID:12410386 PMID:12612583 PMID:15194946 PMID:15917206 PMID:16299064 PMID:16417552 PMID:16822260 PMID:17264970 PMID:17431908 PMID:17632775 PMID:18414213 PMID:18805826 PMID:19773341 PMID:20598277 PMID:20844545 PMID:21520333 PMID:21836662 PMID:22522697 PMID:25167861 PMID:25649377 PMID:25741868 PMID:26404489 PMID:26467025 PMID:27193221 PMID:28133863 PMID:28454995 PMID:28492532 PMID:31064749 NCBI chr  X:156,460,785...156,487,245
Ensembl chr  X:156,463,953...156,487,245
JBrowse link
Mohr Syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Intu inturned planar cell polarity protein ISO ClinVar Annotator: match by term: Mohr syndrome ClinVar PMID:27158779 NCBI chr 2:127,459,089...127,521,327
Ensembl chr 2:127,459,012...127,525,437
JBrowse link
orofaciodigital syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G C2cd3 C2 domain containing 3 centriole elongation regulator ISO CTD Direct Evidence: marker/mechanism CTD PMID:24997988 NCBI chr 1:165,382,279...165,480,088
Ensembl chr 1:165,382,690...165,479,655
JBrowse link
G Ccdc96 coiled-coil domain containing 96 ISO ClinVar Annotator: match by term: Orofaciodigital syndrome ClinVar NCBI chr14:79,443,151...79,445,591
Ensembl chr14:79,443,543...79,445,471
JBrowse link
G Ttc23 tetratricopeptide repeat domain 23 ISO ClinVar Annotator: match by term: Orofaciodigital syndrome ClinVar NCBI chr 1:128,604,324...128,687,900
Ensembl chr 1:128,606,770...128,687,893
JBrowse link
G Wdpcp WD repeat containing planar cell polarity effector ISO ClinVar Annotator: match by term: Orofaciodigital syndromes ClinVar PMID:9536098 PMID:17576681 PMID:20671153 PMID:25326635 PMID:25427950 PMID:25741868 PMID:27158779 PMID:28289185 PMID:28492532 NCBI chr14:106,393,959...106,759,511
Ensembl chr14:106,393,959...106,759,505
JBrowse link
orofaciodigital syndrome I term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ofd1 OFD1, centriole and centriolar satellite protein ISO ClinVar Annotator: match by term: Orofaciodigital syndrome I
ClinVar Annotator: match by term: Oral-Facial-Digital Syndrome Type I
DNA:missense mutation:exon:243C>G (H81Q) (human)
DNA:frameshift mutations, missense mutation, nonsense mutation:multiple
DNA:deletion:exon:c.2183delG (human)
DNA:frameshift mutations, missense mutation, splice-site mutation:multiple
DNA:mutations:exon, intron:multiple
OMIM
ClinVar
PMID:9198060 PMID:9482645 PMID:11179005 PMID:11950863 PMID:16783569 PMID:18414213 PMID:18546297 PMID:22353940 PMID:24884629 PMID:25741868 PMID:26275793 PMID:26467025 PMID:28289185 PMID:28492532 PMID:28973083, PMID:18177199, PMID:16397067, PMID:21729220, PMID:11950863, PMID:23033313 RGD:11535968, RGD:11535966, RGD:11535960, RGD:11535958, RGD:11535957 NCBI chr  X:29,562,165...29,602,934
Ensembl chr  X:29,562,165...29,602,925
JBrowse link
G Tmem17 transmembrane protein 17 ISO ClinVar Annotator: match by term: Orofaciodigital syndrome I ClinVar PMID:25741868 PMID:26982032 NCBI chr14:107,268,235...107,308,546
Ensembl chr14:107,268,128...107,308,542
JBrowse link
orofaciodigital syndrome III term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Celsr2 cadherin, EGF LAG seven-pass G-type receptor 2 ISO ClinVar Annotator: match by term: ORAL-FACIAL-DIGITAL SYNDROME, TYPE III ClinVar NCBI chr 2:211,183,410...211,207,458
Ensembl chr 2:211,183,311...211,207,465
JBrowse link
G Ofd1 OFD1, centriole and centriolar satellite protein ISO ClinVar Annotator: match by term: ORAL-FACIAL-DIGITAL SYNDROME, TYPE III ClinVar NCBI chr  X:29,562,165...29,602,934
Ensembl chr  X:29,562,165...29,602,925
JBrowse link
orofaciodigital syndrome IV term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Tctn3 tectonic family member 3 ISO ClinVar Annotator: match by term: Orofacial-digital syndrome IV
ClinVar Annotator: match by term: MOHR-MAJEWSKI SYNDROME
ClinVar Annotator: match by OMIM:258860
OMIM
ClinVar
PMID:9536098 PMID:17576681 PMID:22883145 PMID:24033266 PMID:25741868 PMID:26092869 PMID:27377014 PMID:28492532 NCBI chr 1:259,681,435...259,691,881
Ensembl chr 1:259,682,249...259,691,742
Ensembl chr 1:259,682,249...259,691,742
JBrowse link
orofaciodigital syndrome IX term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Sclt1 sodium channel and clathrin linker 1 ISO ClinVar Annotator: match by term: Orofaciodigital syndrome 9 ClinVar NCBI chr 2:128,523,376...128,675,668
Ensembl chr 2:128,523,636...128,675,408
JBrowse link
orofaciodigital syndrome V term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ddx59 DEAD-box helicase 59 ISO ClinVar Annotator: match by term: Orofaciodigital syndrome 5
ClinVar Annotator: match by OMIM:174300
OMIM
ClinVar
PMID:23972372 PMID:25741868 NCBI chr13:53,299,872...53,324,824
Ensembl chr13:53,299,872...53,324,824
JBrowse link
Orofaciodigital Syndrome XIV term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G C2cd3 C2 domain containing 3 centriole elongation regulator ISO ClinVar Annotator: match by term: Orofaciodigital syndrome xiv
ClinVar Annotator: match by OMIM:615948
OMIM
ClinVar
PMID:24997988 PMID:25741868 PMID:26092869 PMID:28492532 PMID:30097616 NCBI chr 1:165,382,279...165,480,088
Ensembl chr 1:165,382,690...165,479,655
JBrowse link
Orofaciodigital Syndrome XV term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G RGD1304728 similar to 4933427D14Rik protein ISO ClinVar Annotator: match by term: Orofaciodigital syndrome XV ClinVar
OMIM
PMID:25741868 PMID:26643951 NCBI chr10:58,726,721...58,776,718
Ensembl chr10:58,729,306...58,771,908
JBrowse link
orofaciodigital syndrome XVI term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Tmem107 transmembrane protein 107 ISO ClinVar Annotator: match by term: OROFACIODIGITAL SYNDROME XVI ClinVar
OMIM
PMID:26595381 NCBI chr10:55,653,694...55,656,270
Ensembl chr10:55,653,946...55,656,270
JBrowse link
orofaciodigital syndrome XVII term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Intu inturned planar cell polarity protein ISO ClinVar Annotator: match by term: OROFACIODIGITAL SYNDROME XVII ClinVar
OMIM
PMID:27158779 NCBI chr 2:127,459,089...127,521,327
Ensembl chr 2:127,459,012...127,525,437
JBrowse link
Orofaciodigital Syndrome XVIII term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ift57 intraflagellar transport 57 ISO ClinVar Annotator: match by term: OROFACIODIGITAL SYNDROME XVIII
ClinVar Annotator: match by term: Orofaciodigital syndrome 18
ClinVar
OMIM
PMID:25741868 PMID:27060890 PMID:32860008 NCBI chr11:53,664,638...53,731,779
Ensembl chr11:53,664,638...53,731,779
JBrowse link
Primary Ovarian Insufficiency, Fragile X-Associated term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Aadac arylacetamide deacetylase ISO ClinVar Annotator: match by term: PRIMARY OVARIAN INSUFFICIENCY, FRAGILE X-ASSOCIATED ClinVar PMID:21681106 PMID:25666259 NCBI chr 2:150,146,234...150,157,480
Ensembl chr 2:150,146,234...150,157,480
JBrowse link
G Chd7 chromodomain helicase DNA binding protein 7 ISO ClinVar Annotator: match by term: PRIMARY OVARIAN INSUFFICIENCY, FRAGILE X-ASSOCIATED ClinVar PMID:24033266 PMID:25741868 PMID:28492532 PMID:31042289 NCBI chr 5:21,769,087...21,952,036
Ensembl chr 5:21,830,882...21,950,696
JBrowse link
G Fmr1 FMRP translational regulator 1 ISO RGD PMID:22470123 RGD:12050152 NCBI chr  X:154,684,924...154,722,369
Ensembl chr  X:154,684,935...154,722,314
JBrowse link
G Ntrk1 neurotrophic receptor tyrosine kinase 1 ISO ClinVar Annotator: match by term: PRIMARY OVARIAN INSUFFICIENCY, FRAGILE X-ASSOCIATED ClinVar PMID:25741868 PMID:28492532 NCBI chr 2:187,143,568...187,160,373
Ensembl chr 2:187,143,568...187,160,373
JBrowse link
G Tg thyroglobulin ISO ClinVar Annotator: match by term: PRIMARY OVARIAN INSUFFICIENCY, FRAGILE X-ASSOCIATED ClinVar PMID:8094490 PMID:16187910 PMID:28492532 PMID:31042289 NCBI chr 7:107,467,260...107,652,897
Ensembl chr 7:107,467,260...107,652,899
JBrowse link
Turner syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cat catalase ISO CTD Direct Evidence: marker/mechanism CTD PMID:25101153 NCBI chr 3:93,379,872...93,412,058
Ensembl chr 3:93,379,874...93,412,058
JBrowse link
G Gh1 growth hormone 1 ISO CTD Direct Evidence: therapeutic CTD PMID:15151564 NCBI chr10:94,486,204...94,488,181
Ensembl chr10:94,486,205...94,488,180
JBrowse link
G Igf1 insulin-like growth factor 1 ISO protein:decreased activity:serum: RGD PMID:17067837 RGD:12743588 NCBI chr 7:28,412,123...28,491,815
Ensembl chr 7:28,412,198...28,486,609
JBrowse link
G Igfbp3 insulin-like growth factor binding protein 3 treatment ISO DNA:SNP: :¿¿¿202 A>C(rs2854744)(human) RGD PMID:17067837, PMID:22278433 RGD:12743588, RGD:12743598 NCBI chr14:87,457,647...87,465,374
Ensembl chr14:87,457,647...87,465,374
JBrowse link
G Nos2 nitric oxide synthase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25101153 NCBI chr10:66,188,290...66,221,621
Ensembl chr10:66,189,786...66,313,190
JBrowse link
G Sod1 superoxide dismutase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25101153 NCBI chr11:30,363,282...30,368,858
Ensembl chr11:30,363,280...30,368,862
JBrowse link
G Sod2 superoxide dismutase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:25101153 NCBI chr 1:47,914,757...47,921,587
Ensembl chr 1:47,914,759...47,921,587
JBrowse link
G Vdr vitamin D receptor susceptibility ISO DNA:SNP: :rs7975232(human) RGD PMID:21823528 RGD:13432073 NCBI chr 7:139,344,452...139,394,138
Ensembl chr 7:139,342,063...139,394,166
JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 16909
    Developmental Disease 10557
      Congenital, Hereditary, and Neonatal Diseases and Abnormalities 8872
        Congenital Abnormalities 5180
          chromosomal disease 1746
            Sex Chromosome Disorders 44
              47, XYY Syndrome 0
              49,XXXXX Syndrome 0
              Chromosome Xq Duplication Syndrome 0
              Chromosome Xq28 Duplication Syndrome 0
              Sex Chromosome Disorders of Sex Development + 8
              fragile X syndrome + 20
              orofaciodigital syndrome + 17
paths to the root