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Table 1 XP-CLR CDR genes with evidenced or putative roles in nervous system and neural crest pathways

From: Comparison of village dog and wolf genomes highlights the role of the neural crest in dog domestication

Gene XP-CLR locus (rank) System Phenotypes/effects
RAI1 XP 52 (1st) Xenopus Mutants display craniofacial defects, improper migration of neural crest cells, decrease in facial cartilage components, axonal defects, and altered forebrain ventricle sizes [119].
NKAIN2 (TCBA1) XP 9 (4th) Human Neurocristopathy-like phenotypes observed in patients with translocation breakpoint in NKAIN2 such as hair hypopigmentation, craniofacial and limb malformation, misdevelopment of eyes, and macrocephaly [172].
RNPC3 XP 57 (8th) Human Mutations linked to isolated growth hormone deficiency and pituitary hypoplasia [128].
NPR2 XP 127 (14th) Human, mouse Mutants exhibit dwarfism and impacted skeletal growth during embryogenesis [173, 174].
NPHP3 XP 197 (24th) Mouse, xenopus Left/right asymmetry, shortened body axes, and neural folds fail to close in mutants. Interacts with non-canonical Wnt pathway [84].
LIMCH1 XP 135 (30th) Human Significantly altered methylation patterns in Chinese Han pedigrees exhibiting neural tube defects [175]. LIMCH1 depletion increased cell migration by spatiotemporally regulating non-muscular myosin II activity [176].
CCDC65 XP 215 (45th) Zebrafish Critical for cilia and dynein function. Knockdowns cause left-right asymmetry and axis curvature embryos [177].
DAND5 (cerberus-like) XP 177 (51st) Mouse Prevents signaling of the Nodal pathway on the right side of the developing mouse embryo, establishing left/right asymmetry during early somitogenesis [178].
GBF1 XP 220 (67th) Fly Expressed in embryogenesis, contributes to cell polarity in tubular organs and chemotaxis of neutrophils [179, 180].
GDPD5 XP 181 (102nd) Zebrafish Regulator of the notch signaling pathway, essential for neural crest pathway, linked to body axis determination [181], is induced by retinoids and drives motor neuron differentiation [182].
HAUS3 XP 38 (111th) Zebrafish Essential regulator of embryonic hematopoietic stem/progenitor cell maintenance and cell cycle progression [183].
PAX9 XP 80 (114th) Mouse Mutants displayed improper craniofacial development, lacked organs deriving from pharyngeal pouches, no teeth [184].
DIAPH1 XP 21 (117th) Human Expressed in neural progenitors, linked to microcephaly in humans [185], impacts migration of glioma cells [186].
TCF4 XP 3 (127th) Mouse Myelinates oligodendrocytes, antagonizes the Wnt signaling pathway, and interacts with SOX10 (a known neural crest gene [187]) to promote oligodendrocytic maturation gene expression [188].
TSPAN14 XP 46 (129th) Human Promotes the activity of notch receptors and the expression of ADAM10 [189], both players in the neural crest signaling pathway [190].
SATB2 XP 244 (131st) Mouse Mutants exhibit craniofacial abnormalities (e.g., cleft palate, dental misgrowth) and disrupted osteoblast differentiation [99].
FOXI1 XP 49 (136th) Zebrafish Regulates inner ear and jaw development in embryogenesis, and hypothesized to influence neural crest cell migration and/or separation in the brachial arches [191].
PRKCAB XP 61 (138th) Mouse Mutations yield improper development of the neural tube and spina bifida in mice, asymmetric expansion of hedgehog signaling in the neural tube, impact neuronal cell survival [192].
GNAQ XP 16 (141st) Mouse Mutants exhibit heart malformations and shortened jaws [193].
Tlx3 XP 48 (146th) Mouse Dorsal spinal cord development, specification of glutamatergic neurons [194], and is a target of Wnt signaling pathway [59].
SEMA4A XP 70 (150th) Xenopus Expressed in neurogenic placodes in the developing neural tube, which along with neural crest cells, migrate to final cell locations [195].
TIAM1 XP 225 (154th) Mouse With PAR3, gene is responsible for determination of front-rear and apical-basal polarity in migratory keratinocyte cells [196].
PITX1 XP 124 (157th) Mouse, anolis Transcription factor whose binding sites are near key neural crest signaling members (Wnt, Hedgehog, BMP) [197]. Mutants have improper hind limb development and patterning as well as craniofacial abnormalities [100].
FKBP8 XP 175 (167th) Mouse Critical for development of the neural tube, establishes dorso-ventral patterning, and prevents apoptosis in embryonic cells in the neural tube [198].
AMBRA1 XP 161 (169th) Mouse Mutants show disrupted embryonic development, neural tube defects, cell cycle perturbations (unbalanced proliferation and high apoptosis) [199].
SCUBE1 XP 115 (202nd) Mouse Required for proper development of the central nervous system, neural tube, brain regions, and the cranial vault formation [200].
CYP1B1 XP 152 (229th) Zebrafish Mutants showed disrupted neural crest migration [201] and is associated with retinoic acid synthesis during the patterning of the developing embryo [50].
  1. Genes within XP-CLR candidate domestication regions (with rank) that have experimental or clinical evidence that illustrate roles in early embryonic pathways, especially in the developing central nervous system and components of the neural crest and its signaling pathways