Table 1. Genes within each confirmed de novo CNV region. Genes that are in the RefSeq database http://www.ncbi.nlm.nih.gov/gene as well as in the Ensembl database http://www.ensembl.org are reported.
| Gene ID | Description | Tissue expressed (transcripts per million) a | Gene ontology (functioning of gene products) b |
|---|---|---|---|
| chr15: 18 728 578–19 399 146 | |||
| HERC2P3 | Hect domain and RLD 2 pseudogene 3, non-coding RNA | Brain (69); Thyroid (42); Uterus (38); Thymus (36); Testis (24); Pharynx (24); Mammary Gland (13); Stomach (10); Placenta (10); Eye (9); Blood (8); Connective Tissue (6); Prostate (5); Embryonic Tissue (4); Intestine (4); Kidney (4); Liver (4); Skin (4) | Molecular functions: metal ion binding; ubiquitin-protein ligase activity. |
| chr4: 189 928 060–191 261 904 | |||
| HSP90AA4P | Heat shock protein 90kDa alpha (cytosolic), class A member 4, pseudogene, non-coding RNA | Ascites (24); Skin (4) | Cellular components: cytoplasm.Molecular functions: ATP binding; nucleotide binding; unfolded protein binding.Biological processes: protein folding; response to stress. |
| FRG1 | FSHD region gene 1, mRNA | Bone Marrow (143); Pharynx (72); Pituitary Gland (60); Blood (56); Lymph Node (54); Salivary Gland (49); Ovary (48); Parathyroid (48); Eye (47); Muscle (46); Liver (33); Mammary Gland (32); Stomach (31); Uterus (30); Adrenal Gland (30); Embryonic Tissue (27); Lung (26); Prostate (21); Testis (21); Cervix (20); Connective Tissue (20); Pancreas (18); Kidney (14); Skin (14); Bone (13); Heart (11); Intestine (8); Brain (4); Placenta (3) | Cellular components: cajal body; catalytic step 2 spliceosome; nuclear speck; nucleolus; nucleus.Biological processes: nuclear mRNA splicing, via spliceosome; RNA splicing; rRNA processing. |
| TUBB4Q | Tubulin, beta polypeptide 4, member Q, pseudogene, mRNA | Skin (4) | Cellular components: cytoplasm; cytoskeleton; microtubule. Molecular functions: GTP binding; GTPase activity; nucleotide-binding; structural molecule activity Biological processes: ‘de novo' posttranslational protein folding; cellular protein metabolic process; microtubule-based movement; protein folding; protein polymerization. |
| FRG2 | FSHD region gene 2, mRNA | NA | Cellular components: nucleus. |
| DUX4 family | double homeobox 4, mRNA | NA | Cellular components: nucleus. |
| Molecular functions: sequence-specific DNA binding; sequence-specific DNA binding transcription factor activity. | |||
| chr17: 5 864 185–5 980 521 | |||
| WSCD1 | WSC domain containing 1, mRNA | Muscle (120); Umbilical Cord (73); Pituitary Gland (60); Eye (56); Testis (48); Brain (45); Kidney (37); Ovary (29); Thyroid (21); Bone Marrow (20); Vascular (19); Embryonic Tissue (18); Spleen (18); Placenta (17); Lung (14); Mouth (14); Bone (13); Connective Tissue (13); Heart (11); Pancreas (9); Blood (8) | Cellular components: integral to membrane (ie, penetrating at least one phospholipid bilayer of a membrane); membrane (ie, double layer of lipid molecules that encloses all cells, and many organelles; may be a single or double lipid bilayer; also includes associated proteins)Molecular functions: sulphotransferase activity. |
Abbreviations: FSHD, facioscapulohumeral muscular dystrophy; NA, tissue-specific gene expression data not available.
a
Data from NCBI UniGene http://www.ncbi.nlm.nih.gov/unigene.
b
Data from the Gene Ontology Project http://www.geneontology.org.