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Abstract

Most known disease-causing mutations occur in protein-coding regions of DNA. While some of these involve a loss of protein function (e.g., through premature stop codons or missense changes that destabilize protein folding), many act via alternative molecular mechanisms and have dominant-negative or gain-of-function effects. In nearly all cases, these non-loss-of-function mutations can be understood by considering interactions of the wild-type and mutant protein with other molecules, such as proteins, nucleic acids, or small ligands and substrates. Here, we review the diverse molecular mechanisms by which pathogenic mutations can have non-loss-of-function effects, including by disrupting interactions, increasing binding affinity, changing binding specificity, causing assembly-mediated dominant-negative and dominant-positive effects, creating novel interactions, and promoting aggregation and phase separation. We believe that increased awareness of these diverse molecular disease mechanisms will lead to improved diagnosis (and ultimately treatment) of human genetic disorders.

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2022-08-31
2024-04-19
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Literature Cited

  1. 1.
    Abell AN, DeCathelineau AM, Weed SA, Ambruso DR, Riches DW, Johnson GL. 2004. Rac2D57N, a dominant inhibitory Rac2 mutant that inhibits p38 kinase signaling and prevents surface ruffling in bone-marrow-derived macrophages. J. Cell Sci. 117:243–55
    [Google Scholar]
  2. 2.
    Abriata LA, Palzkill T, Dal Peraro M. 2015. How structural and physicochemical determinants shape sequence constraints in a functional enzyme. PLOS ONE 10:e0118684
    [Google Scholar]
  3. 3.
    Aiken J, Buscaglia G, Aiken AS, Moore JK, Bates EA. 2020. Tubulin mutations in brain development disorders: why haploinsufficiency does not explain TUBA1A tubulinopathies. Cytoskeleton 77:40–54
    [Google Scholar]
  4. 4.
    Alberti S, Gladfelter A, Mittag T. 2019. Considerations and challenges in studying liquid-liquid phase separation and biomolecular condensates. Cell 176:419–34
    [Google Scholar]
  5. 5.
    Ali MH, Imperiali B. 2005. Protein oligomerization: how and why. Bioorg. Med. Chem. 13:5013–20
    [Google Scholar]
  6. 6.
    Ambruso DR, Knall C, Abell AN, Panepinto J, Kurkchubasche A et al. 2000. Human neutrophil immunodeficiency syndrome is associated with an inhibitory Rac2 mutation. PNAS 97:4654–59
    [Google Scholar]
  7. 7.
    Baek M, DiMaio F, Anishchenko I, Dauparas J, Ovchinnikov S et al. 2021. Accurate prediction of protein structures and interactions using a three-track neural network. Science 373:871–76
    [Google Scholar]
  8. 8.
    Balog EM, Fruen BR, Shomer NH, Louis CF. 2001. Divergent effects of the malignant hyperthermia-susceptible Arg615→Cys mutation on the Ca2+ and Mg2+ dependence of the RyR1. Biophys. J. 81:2050–58
    [Google Scholar]
  9. 9.
    Bergendahl LT, Gerasimavicius L, Miles J, Macdonald L, Wells JN et al. 2019. The role of protein complexes in human genetic disease. Protein Sci 28:1400–11
    [Google Scholar]
  10. 10.
    Bergendahl LT, Marsh JA. 2017. Functional determinants of protein assembly into homomeric complexes. Sci. Rep. 7:4932
    [Google Scholar]
  11. 11.
    Berthelot K, Cullin C, Lecomte S. 2013. What does make an amyloid toxic: morphology, structure or interaction with membrane?. Biochimie 95:12–19
    [Google Scholar]
  12. 12.
    Beryozkin A, Shevah E, Kimchi A, Mizrahi-Meissonnier L, Khateb S et al. 2015. Whole exome sequencing reveals mutations in known retinal disease genes in 33 out of 68 Israeli families with inherited retinopathies. Sci. Rep. 5:13187
    [Google Scholar]
  13. 13.
    Bledsoe RK, Madauss KP, Holt JA, Apolito CJ, Lambert MH et al. 2005. A ligand-mediated hydrogen bond network required for the activation of the mineralocorticoid receptor. J. Biol. Chem. 280:31283–93
    [Google Scholar]
  14. 14.
    Borooah S, Stanton CM, Marsh J, Carss KJ, Waseem N et al. 2018. Whole genome sequencing reveals novel mutations causing autosomal dominant inherited macular degeneration. Ophthalmic Genet 39:763–70
    [Google Scholar]
  15. 15.
    Boyer DR, Li B, Sun C, Fan W, Sawaya MR et al. 2019. Structures of fibrils formed by α-synuclein hereditary disease mutant H50Q reveal new polymorphs. Nat. Struct. Mol. Biol. 26:1044–52
    [Google Scholar]
  16. 16.
    Boyer DR, Li B, Sun C, Fan W, Zhou K et al. 2020. The α-synuclein hereditary mutation E46K unlocks a more stable, pathogenic fibril structure. PNAS 117:3592–602
    [Google Scholar]
  17. 17.
    Brás IC, Xylaki M, Outeiro TF. 2020. Mechanisms of alpha-synuclein toxicity: an update and outlook. Prog. Brain Res. 252:91–129
    [Google Scholar]
  18. 18.
    Burley SK, Berman HM, Bhikadiya C, Bi C, Chen L et al. 2019. Protein Data Bank: the single global archive for 3D macromolecular structure data. Nucleic Acids Res 47:D520–28
    [Google Scholar]
  19. 19.
    Cantley LC. 2002. The phosphoinositide 3-kinase pathway. Science 296:1655–57
    [Google Scholar]
  20. 20.
    Carvill GL, Matheny T, Hesselberth J, Demarest S. 2021. Haploinsufficiency, dominant negative, and gain-of-function mechanisms in epilepsy: matching therapeutic approach to the pathophysiology. Neurotherapeutics 18:1500–14
    [Google Scholar]
  21. 21.
    Cavaco BM, Canaff L, Nolin-Lapalme A, Vieira M, Silva TN et al. 2018. Homozygous calcium-sensing receptor polymorphism R544Q presents as hypocalcemic hypoparathyroidism. J. Clin. Endocrinol. Metab. 103:2879–88
    [Google Scholar]
  22. 22.
    Chang YF, Imam JS, Wilkinson MF. 2007. The nonsense-mediated decay RNA surveillance pathway. Annu. Rev. Biochem. 76:51–74
    [Google Scholar]
  23. 23.
    Chen B, Altman RB. 2017. Opportunities for developing therapies for rare genetic diseases: focus on gain-of-function and allostery. Orphanet J. Rare Dis. 12:61
    [Google Scholar]
  24. 24.
    Chen S, Wang QL, Xu S, Liu I, Li LY et al. 2002. Functional analysis of cone-rod homeobox (CRX) mutations associated with retinal dystrophy. Hum. Mol. Genet. 11:873–84
    [Google Scholar]
  25. 25.
    Chirasani VR, Xu L, Addis HG, Pasek DA, Nikolay X et al. 2019. A central core disease mutation in the Ca2+-binding site of skeletal muscle ryanodine receptor impairs single-channel regulation. Am. J. Physiol. Cell Physiol. 317:358–65
    [Google Scholar]
  26. 26.
    Clark AR, Naylor CE, Bagnéris C, Keep NH, Slingsby C. 2011. Crystal structure of R120G disease mutant of human αB-crystallin domain dimer shows closure of a groove. J. Mol. Biol. 408:118–34
    [Google Scholar]
  27. 27.
    Coffill CR, Muller PAJ, Oh HK, Neo SP, Hogue KA et al. 2012. Mutant p53 interactome identifies nardilysin as a p53R273H-specific binding partner that promotes invasion. EMBO Rep 13:638–44
    [Google Scholar]
  28. 28.
    Cool RH, Schmidt G, Lenzen CU, Prinz H, Vogt D, Wittinghofer A. 1999. The Ras mutant D119N is both dominant negative and activated. Mol. Cell. Biol. 19:6297–305
    [Google Scholar]
  29. 29.
    David A, Sternberg MJE. 2015. The contribution of missense mutations in core and rim residues of protein-protein interfaces to human disease. J. Mol. Biol. 427:2886–98
    [Google Scholar]
  30. 30.
    De Wet H, Rees MG, Shimomura K, Aittoniemi J, Patch AM et al. 2007. Increased ATPase activity produced by mutations at arginine-1380 in nucleotide-binding domain 2 of ABCC8 causes neonatal diabetes. PNAS 104:18988–92
    [Google Scholar]
  31. 31.
    Dedov VN, Dedova IV, Merrill AH, Nicholson GA. 2004. Activity of partially inhibited serine palmitoyltransferase is sufficient for normal sphingolipid metabolism and viability of HSN1 patient cells. Biochim. Biophys. Acta Mol. Basis Dis. 1688:168–75
    [Google Scholar]
  32. 32.
    des Georges A, Clarke OB, Zalk R, Yuan Q, Condon KJ et al. 2016. Structural basis for gating and activation of RyR1. Cell 167:145–57.e17
    [Google Scholar]
  33. 33.
    Di Salvo ML, Ko TP, Musayev FN, Raboni S, Schirch V, Safo MK. 2002. Active site structure and stereospecificity of Escherichia coli pyridoxine-5′-phosphate oxidase. J. Mol. Biol. 315:385–97
    [Google Scholar]
  34. 34.
    Douse CH, Bloor S, Liu Y, Shamin M, Tchasovnikarova IA et al. 2018. Neuropathic MORC2 mutations perturb GHKL ATPase dimerization dynamics and epigenetic silencing by multiple structural mechanisms. Nat. Commun. 9:651
    [Google Scholar]
  35. 35.
    Drutman SB, Haerynck F, Zhong FL, Hum D, Hernandez NJ et al. 2019. Homozygous NLRP1 gain-of-function mutation in siblings with a syndromic form of recurrent respiratory papillomatosis. PNAS 116:19055–63
    [Google Scholar]
  36. 36.
    Endo M. 2009. Calcium-induced calcium release in skeletal muscle. Physiol. Rev. 89:1153–76
    [Google Scholar]
  37. 37.
    Erxleben C, Liao Y, Gentile S, Chin D, Gomez-Alegria C et al. 2006. Cyclosporin and Timothy syndrome increase mode 2 gating of CaV1.2 calcium channels through aberrant phosphorylation of S6 helices. PNAS 103:3932–37
    [Google Scholar]
  38. 38.
    Fernández-Velasco M, Rueda A, Rizzi N, Benitah JP, Colombi B et al. 2009. Increased Ca2+ sensitivity of the ryanodine receptor mutant RyR2R4496C underlies catecholaminergic polymorphic ventricular tachycardia. Circ. Res. 104:201–9
    [Google Scholar]
  39. 39.
    Friedrich C, Rinné S, Zumhagen S, Kiper AK, Silbernagel N et al. 2014. Gain-of-function mutation in TASK-4 channels and severe cardiac conduction disorder. EMBO Mol. Med. 6:937–51
    [Google Scholar]
  40. 40.
    Gable K, Gupta SD, Han G, Niranjanakumari S, Harmon JM, Dunn TM. 2010. A disease-causing mutation in the active site of serine palmitoyltransferase causes catalytic promiscuity. J. Biol. Chem. 285:22846–52
    [Google Scholar]
  41. 41.
    Gao M, Zhou H, Skolnick J. 2015. Insights into disease-associated mutations in the human proteome through protein structural analysis. Structure 23:1362–69
    [Google Scholar]
  42. 42.
    Gerasimavicius L, Liu X, Marsh JA. 2020. Identification of pathogenic missense mutations using protein stability predictors. Sci. Rep. 10:15387
    [Google Scholar]
  43. 43.
    Gerasimavicius L, Livesey BJ, Marsh JA. 2021. Loss-of-function, gain-of-function and dominant-negative mutations have profoundly different effects on protein structure: implications for variant effect prediction. bioRxiv 2021.10.23.465554. https://doi.org/10.1101/2021.10.23.465554
    [Crossref]
  44. 44.
    Gerber S, Alzayady KJ, Burglen L, Brémond-Gignac D, Marchesin V et al. 2016. Recessive and dominant de novo ITPR1 mutations cause Gillespie syndrome. Am. J. Hum. Genet. 98:971–80
    [Google Scholar]
  45. 45.
    Golovleva I, Bhattacharya S, Wu Z, Shaw N, Yang Y et al. 2003. Disease-causing mutations in the cellular retinaldehyde binding protein tighten and abolish ligand interactions. J. Biol. Chem. 278:12397–402
    [Google Scholar]
  46. 46.
    Gopalakrishna KN, Boyd K, Yadav RP, Artemyev NO. 2016. Aryl hydrocarbon receptor-interacting protein-like 1 is an obligate chaperone of phosphodiesterase 6 and is assisted by the γ-subunit of its client. J. Biol. Chem. 291:16282–91
    [Google Scholar]
  47. 47.
    Grasberger H, Ringkananont U, LeFrancois P, Abramowicz M, Vassart G, Refetoff S. 2005. Thyroid transcription factor 1 rescues PAX8/p300 synergism impaired by a natural PAX8 paired domain mutation with dominant negative activity. Mol. Endocrinol. 19:1779–91
    [Google Scholar]
  48. 48.
    Gress A, Ramensky V, Kalinina OV. 2017. Spatial distribution of disease-associated variants in three-dimensional structures of protein complexes. Oncogenesis 6:e380
    [Google Scholar]
  49. 49.
    Grueninger D, Treiber N, Ziegler MOP, Koetter JWA, Schulze MS, Schulz GE. 2008. Designed protein-protein association. Science 319:206–9
    [Google Scholar]
  50. 50.
    Gu Y, Jia B, Yang FC, D'Souza M, Harris CE et al. 2001. Biochemical and biological characterization of a human Rac2 GTPase mutant associated with phagocytic immunodeficiency. J. Biol. Chem. 276:15929–38
    [Google Scholar]
  51. 51.
    Hamajima N, Johmura Y, Suzuki S, Nakanishi M, Saitoh S. 2013. Increased protein stability of CDKN1C causes a gain-of-function phenotype in patients with IMAGe syndrome. PLOS ONE 8:e75137
    [Google Scholar]
  52. 52.
    Han G, Gupta SD, Gable K, Niranjanakumari S, Moitra P et al. 2009. Identification of small subunits of mammalian serine palmitoyltransferase that confer distinct acyl-CoA substrate specificities. PNAS 106:8186–91
    [Google Scholar]
  53. 53.
    Hao Y, Wang C, Cao B, Hirsch BM, Song J et al. 2013. Gain of interaction with IRS1 by p110α-helical domain mutants is crucial for their oncogenic functions. Cancer Cell 23:583–93
    [Google Scholar]
  54. 54.
    Hedrich UBS, Lauxmann S, Wolff M, Synofzik M, Bast T et al. 2021. 4-Aminopyridine is a promising treatment option for patients with gain-of-function KCNA2-encephalopathy. Sci. Transl. Med. 13:4957
    [Google Scholar]
  55. 55.
    Heldin CH. 1995. Dimerization of cell surface receptors in signal transduction. Cell 80:213–23
    [Google Scholar]
  56. 56.
    Heyn P, Logan CV, Fluteau A, Challis RC, Auchynnikava T et al. 2019. Gain-of-function DNMT3A mutations cause microcephalic dwarfism and hypermethylation of Polycomb-regulated regions. Nat. Genet. 51:96–105
    [Google Scholar]
  57. 57.
    Hipp MS, Park SH, Hartl UU. 2014. Proteostasis impairment in protein-misfolding and -aggregation diseases. Trends Cell Biol 24:506–14
    [Google Scholar]
  58. 58.
    Hornemann T, Penno A, Richard S, Nicholson G, Van Dijk FS et al. 2009. A systematic comparison of all mutations in hereditary sensory neuropathy type I (HSAN I) reveals that the G387A mutation is not disease associated. Neurogenetics 10:135–43
    [Google Scholar]
  59. 59.
    Hu Z, Wan X, Hao R, Zhang H, Li L et al. 2015. Phosphorylation of mutationally introduced tyrosine in the activation loop of HER2 confers gain-of-function activity. PLOS ONE 10:e0123623
    [Google Scholar]
  60. 60.
    Iyer KA, Hu Y, Nayak AR, Kurebayashi N, Murayama T, Samsó M. 2020. Structural mechanism of two gain-of-function cardiac and skeletal RyR mutations at an equivalent site by cryo-EM. Sci. Adv. 6:eabb2964
    [Google Scholar]
  61. 61.
    Johansson EDB, Jonasson L-E. 1971. Progesterone levels in amniotic fluid and plasma from women. I. Levels during normal pregnancy. Acta Obstet. Gynecol. Scand. 50:339–43
    [Google Scholar]
  62. 62.
    Jubb HC, Pandurangan AP, Turner MA, Ochoa-Montaño B, Blundell TL, Ascher DB. 2017. Mutations at protein-protein interfaces: Small changes over big surfaces have large impacts on human health. Prog. Biophys. Mol. Biol. 128:3–13
    [Google Scholar]
  63. 63.
    Jumper J, Evans R, Pritzel A, Green T, Figurnov M et al. 2021. Highly accurate protein structure prediction with AlphaFold. Nature 596:583–89
    [Google Scholar]
  64. 64.
    Kakizawa S, Yamazawa T, Chen Y, Ito A, Murayama T et al. 2012. Nitric oxide-induced calcium release via ryanodine receptors regulates neuronal function. EMBO J 31:417–28
    [Google Scholar]
  65. 65.
    Knowles TPJ, Vendruscolo M, Dobson CM. 2014. The amyloid state and its association with protein misfolding diseases. Nat. Rev. Mol. Cell Biol. 15:384–96
    [Google Scholar]
  66. 66.
    Kontaridis MI, Swanson KD, David FS, Barford D, Neel BG. 2006. PTPN11 (Shp2) mutations in LEOPARD syndrome have dominant negative, not activating, effects. J. Biol. Chem. 281:6785–92
    [Google Scholar]
  67. 67.
    Lanner JT, Georgiou DK, Joshi AD, Hamilton SL. 2010. Ryanodine receptors: structure, expression, molecular details, and function in calcium release. Cold Spring Harb. Perspect. Biol. 2:a003996
    [Google Scholar]
  68. 68.
    Larson HN, Weiner H, Hurley TD. 2005. Disruption of the coenzyme binding site and dimer interface revealed in the crystal structure of mitochondrial aldehyde dehydrogenase “Asian” variant. J. Biol. Chem. 280:30550–56
    [Google Scholar]
  69. 69.
    Leen WG, Klepper J, Verbeek MM, Leferink M, Hofste T et al. 2010. Glucose transporter-1 deficiency syndrome: the expanding clinical and genetic spectrum of a treatable disorder. Brain 133:655–70
    [Google Scholar]
  70. 70.
    Leferink NGH, Antonyuk SV, Houwman JA, Scrutton NS, Eady RR, Hasnain SS. 2014. Impact of residues remote from the catalytic centre on enzyme catalysis of copper nitrite reductase. Nat. Commun. 5:4395
    [Google Scholar]
  71. 71.
    Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E et al. 2016. Analysis of protein-coding genetic variation in 60,706 humans. Nature 536:285–91
    [Google Scholar]
  72. 72.
    Levy ED. 2010. A simple definition of structural regions in proteins and its use in analyzing interface evolution. J. Mol. Biol. 403:660–70
    [Google Scholar]
  73. 73.
    Livesey BJ, Marsh JA. 2021. The properties of human disease mutations at protein interfaces. bioRxiv 2021.08.20.457107. https://doi.org/10.1101/2021.08.20.457107
    [Crossref]
  74. 74.
    Luscieti S, Santambrogio P, D'Estaintot BL, Granier T, Cozzi A et al. 2010. Mutant ferritin L-chains that cause neurodegeneration act in a dominant-negative manner to reduce ferritin iron incorporation. J. Biol. Chem. 285:11948–57
    [Google Scholar]
  75. 75.
    Majumder A, Gopalakrishna KN, Cheguru P, Gakhar L, Artemyev NO. 2013. Interaction of aryl hydrocarbon receptor-interacting protein-like 1 with the farnesyl moiety. J. Biol. Chem. 288:21320–28
    [Google Scholar]
  76. 76.
    Marsh JA, Teichmann SA. 2015. Structure, dynamics, assembly, and evolution of protein complexes. Annu. Rev. Biochem. 84:551–75
    [Google Scholar]
  77. 77.
    McEntagart M, Williamson KA, Rainger JK, Wheeler A, Seawright A et al. 2016. A restricted repertoire of de novo mutations in ITPR1 cause Gillespie syndrome with evidence for dominant-negative effect. Am. J. Hum. Genet. 98:981–92
    [Google Scholar]
  78. 78.
    McRae JF, Clayton S, Fitzgerald TW, Kaplanis J, Prigmore E et al. 2017. Prevalence and architecture of de novo mutations in developmental disorders. Nature 542:433–38
    [Google Scholar]
  79. 79.
    Meij IC, Koenderink JB, Van Bokhoven H, Assink KFH, Tiel Groenestege W et al. 2000. Dominant isolated renal magnesium loss is caused by misrouting of the Na+,K+-ATPase γ-subunit. Nat. Genet. 26:265–66
    [Google Scholar]
  80. 80.
    Meissner G, Rios E, Tripathy A, Pasek DA. 1997. Regulation of skeletal muscle Ca2+ release channel (ryanodine receptor) by Ca2+ and monovalent cations and anions. J. Biol. Chem. 272:1628–38
    [Google Scholar]
  81. 81.
    Meli AC, Refaat MM, Dura M, Reiken S, Wronska A et al. 2011. A novel ryanodine receptor mutation linked to sudden death increases sensitivity to cytosolic calcium. Circ. Res. 109:281–90
    [Google Scholar]
  82. 82.
    Meyer K, Kirchner M, Uyar B, Cheng JY, Russo G et al. 2018. Mutations in disordered regions can cause disease by creating dileucine motifs. Cell 175:239–53.e17
    [Google Scholar]
  83. 83.
    Moncada-Vélez M, Martinez-Barricarte R, Bogunovic D, Kong XF, Blancas-Galicia L et al. 2013. Partial IFN-γR2 deficiency is due to protein misfolding and can be rescued by inhibitors of glycosylation. Blood 122:2390–401
    [Google Scholar]
  84. 84.
    Mosca R, Pache RA, Aloy P. 2012. The role of structural disorder in the rewiring of protein interactions through evolution. Mol. Cell. Proteom. 11:M111.014969–18
    [Google Scholar]
  85. 85.
    Murayama T, Kurebayashi N, Ogawa Y. 2000. Role of Mg2+ in Ca2+-induced Ca2+ release through ryanodine receptors of frog skeletal muscle: modulations by adenine nucleotides and caffeine. Biophys. J. 78:1810–24
    [Google Scholar]
  86. 86.
    Murayama T, Ogawa H, Kurebayashi N, Ohno S, Horie M, Sakurai T. 2018. A tryptophan residue in the caffeine-binding site of the ryanodine receptor regulates Ca2+ sensitivity. Commun. Biol. 1:98
    [Google Scholar]
  87. 87.
    Musayev FN, Di Salvo ML, Saavedra MA, Contestabile R, Ghatge MS et al. 2009. Molecular basis of reduced pyridoxine 5′-phosphate oxidase catalytic activity in neonatal epileptic encephalopathy disorder. J. Biol. Chem. 284:30949–56
    [Google Scholar]
  88. 88.
    Naik MU, Stalker TJ, Brass LF, Naik UP. 2012. JAM-A protects from thrombosis by suppressing integrin αIIbβ3-dependent outside-in signaling in platelets. Blood 119:3352–60
    [Google Scholar]
  89. 89.
    Nakai J, Ogura T, Protasi F, Franzini-Armstrong C, Allen PD, Beam KG. 1997. Functional nonequality of the cardiac and skeletal ryanodine receptors. PNAS 94:1019–22
    [Google Scholar]
  90. 90.
    Natan E, Wells JN, Teichmann SA, Marsh JA. 2017. Regulation, evolution and consequences of cotranslational protein complex assembly. Curr. Opin. Struct. Biol. 42:90–97
    [Google Scholar]
  91. 91.
    Pan YE, Tibbe D, Harms FL, Reißner C, Becker K et al. 2021. Missense mutations in CASK, coding for the calcium-/calmodulin-dependent serine protein kinase, interfere with neurexin binding and neurexin-induced oligomerization. J. Neurochem. 157:1331–50
    [Google Scholar]
  92. 92.
    Pandey KN. 2009. Functional roles of short sequence motifs in the endocytosis of membrane receptors. Front. Biosci. 14:5339–60
    [Google Scholar]
  93. 93.
    Parker RO, Crouch RK. 2010. Retinol dehydrogenases (RDHs) in the visual cycle. Exp. Eye Res. 91:788–92
    [Google Scholar]
  94. 94.
    Perica T, Mathy CJP, Xu J, Jang G, Zhang Y et al. 2021. Systems-level effects of allosteric perturbations to a model molecular switch. Nature 599:152–57
    [Google Scholar]
  95. 95.
    Pires DEV, Blundell TL, Ascher DB. 2016. MCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance. Sci. Rep. 6:29575
    [Google Scholar]
  96. 96.
    Prockop DJ, Constantinou CD, Dombrowski KE, Hojima Y, Kadler KE et al. 1989. Type I procollagen: the gene-protein system that harbors most of the mutations causing osteogenesis imperfecta and probably more common heritable disorders of connective tissue. Am. J. Med. Genet. 34:60–67
    [Google Scholar]
  97. 97.
    Radaelli G, de Souza Santos F, Borelli WV, Pisani L, Nunes ML et al. 2018. Causes of mortality in early infantile epileptic encephalopathy: a systematic review. Epilepsy Behav 85:32–36
    [Google Scholar]
  98. 98.
    Rafestin-Oblin M-E, Souque A, Bocchi B, Pinon G, Fagart J, Vandewalle A. 2003. The severe form of hypertension caused by the activating S810L mutation in the mineralocorticoid receptor is cortisone related. Endocrinology 144:528–33
    [Google Scholar]
  99. 99.
    Rogerson FM, Fuller PJ. 2000. Mineralocorticoid action. Steroids 65:61–73
    [Google Scholar]
  100. 100.
    Rosowski EE, Deng Q, Keller NP, Huttenlocher A. 2016. Rac2 functions in both neutrophils and macrophages to mediate motility and host defense in larval zebrafish. J. Immunol. 197:4780–90
    [Google Scholar]
  101. 101.
    Rotthier A, Penno A, Rautenstrauss B, Auer-Grumbach M, Stettner GM et al. 2011. Characterization of two mutations in the SPTLC1 subunit of serine palmitoyltransferase associated with hereditary sensory and autonomic neuropathy type I. Hum. Mutat. 32:E2211–25
    [Google Scholar]
  102. 102.
    Sahni N, Yi S, Taipale M, Fuxman Bass JI, Coulombe-Huntington J et al. 2015. Widespread macromolecular interaction perturbations in human genetic disorders. Cell 161:647–60
    [Google Scholar]
  103. 103.
    Schmidt G, Lenzen C, Simon I, Deuter R, Cool RH et al. 1996. Biochemical and biological consequences of changing the specificity of p21ras from guanosine to xanthosine nucleotides. Oncogene 12:87–96
    [Google Scholar]
  104. 104.
    Schneider MF. 1994. Control of calcium release in functioning skeletal muscle fibers. Annu. Rev. Physiol. 56:463–84
    [Google Scholar]
  105. 105.
    Scita G, Tenca P, Frittoli E, Tocchettti A, Innocenti M et al. 2000. Signaling from Ras to Rac and beyond: not just a matter of GEFs. EMBO J 19:2393–98
    [Google Scholar]
  106. 106.
    Sheikh TI, Ausió J, Faghfoury H, Silver J, Lane JB et al. 2016. From function to phenotype: impaired DNA binding and clustering correlates with clinical severity in males with missense mutations in MECP2. Sci. Rep. 6:38590
    [Google Scholar]
  107. 107.
    Stanton CM, Borooah S, Drake C, Marsh JA, Campbell S et al. 2017. Novel pathogenic mutations in C1QTNF5 support a dominant negative disease mechanism in late-onset retinal degeneration. Sci. Rep. 7:12147
    [Google Scholar]
  108. 108.
    Stefl S, Nishi H, Petukh M, Panchenko AR, Alexov E 2013. Molecular mechanisms of disease-causing missense mutations. J. Mol. Biol. 425:3919–36
    [Google Scholar]
  109. 109.
    Stenson PD, Mort M, Ball EV, Evans K, Hayden M et al. 2017. The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies. Hum. Genet. 136:665–77
    [Google Scholar]
  110. 110.
    Steward RE, MacArthur MW, Laskowski RA, Thornton JM. 2003. Molecular basis of inherited diseases: a structural perspective. Trends Genet 19:505–13
    [Google Scholar]
  111. 111.
    Sun Y, Hou S, Zhao K, Long H, Liu Z et al. 2020. Cryo-EM structure of full-length α-synuclein amyloid fibril with Parkinson's disease familial A53T mutation. Cell Res 30:360–62
    [Google Scholar]
  112. 112.
    Sun Y, Long H, Xia W, Wang K, Zhang X et al. 2021. The hereditary mutation G51D unlocks a distinct fibril strain transmissible to wild-type α-synuclein. Nat. Commun. 12:6252
    [Google Scholar]
  113. 113.
    Taniguchi H, Fujimoto A, Kono H, Furuta M, Fujita M, Nakagawa H. 2018. Loss-of-function mutations in Zn-finger DNA-binding domain of HNF4A cause aberrant transcriptional regulation in liver cancer. Oncotarget 9:26144–56
    [Google Scholar]
  114. 114.
    Tchasovnikarova IA, Timms RT, Douse CH, Roberts RC, Dougan G et al. 2017. Hyperactivation of HUSH complex function by Charcot-Marie-Tooth disease mutation in MORC2. Nat. Genet. 49:1035–44
    [Google Scholar]
  115. 115.
    Tompa P, Davey NE, Gibson TJ, Babu MM. 2014. A million peptide motifs for the molecular biologist. Mol. Cell 55:161–69
    [Google Scholar]
  116. 116.
    Tong L, De Vos AM, Milburn MV, Jancarik J, Noguchi S et al. 1989. Structural differences between a ras oncogene protein and the normal protein. Nature 337:90–93
    [Google Scholar]
  117. 117.
    Tyzack JD, Furnham N, Sillitoe I, Orengo CM, Thornton JM. 2017. Understanding enzyme function evolution from a computational perspective. Curr. Opin. Struct. Biol. 47:131–39
    [Google Scholar]
  118. 118.
    Ueda K, Nakamura K, Hayashi T, Inagaki N, Takahashi M et al. 2004. Functional characterization of a trafficking-defective HCN4 mutation, D553N, associated with cardiac arrhythmia. J. Biol. Chem. 279:27194–98
    [Google Scholar]
  119. 119.
    Vacic V, Markwick PRL, Oldfield CJ, Zhao X, Haynes C et al. 2012. Disease-associated mutations disrupt functionally important regions of intrinsic protein disorder. PLOS Comput. Biol. 8:e1002709
    [Google Scholar]
  120. 120.
    Vadas O, Burke JE, Zhang X, Berndt A, Williams RL. 2011. Structural biology structural basis for activation and inhibition of class I phosphoinositide 3-kinases. Sci. Signal. 4:re2
    [Google Scholar]
  121. 121.
    Veitia RA. 2007. Exploring the molecular etiology of dominant-negative mutations. Plant Cell 19:3843–51
    [Google Scholar]
  122. 122.
    Vogt G, Chapgier A, Yang K, Chuzhanova N, Feinberg J et al. 2005. Gains of glycosylation comprise an unexpectedly large group of pathogenic mutations. Nat. Genet. 37:692–700
    [Google Scholar]
  123. 123.
    Vogt G, Vogt B, Chuzhanova N, Julenius K, Cooper DN, Casanova JL. 2007. Gain-of-glycosylation mutations. Curr. Opin. Genet. Dev. 17:245–51
    [Google Scholar]
  124. 124.
    Walter M, Clark SG, Levinson AD. 1986. The oncogenic activation of human p21ras by a novel mechanism. Science 233:649–52
    [Google Scholar]
  125. 125.
    Wang Y, Thomas A, Lau C, Rajan A, Zhu Y et al. 2014. Mutations of epigenetic regulatory genes are common in thymic carcinomas. Sci. Rep. 4:7336
    [Google Scholar]
  126. 126.
    Williams DA, Tao W, Yang F, Kim C, Gu Y et al. 2000. Dominant negative mutation of the hematopoietic-specific Rho GTPase, Rac2, is associated with a human phagocyte immunodeficiency. Blood 96:1646–54
    [Google Scholar]
  127. 127.
    Williamson KA, Hall HN, Owen LJ, Livesey BJ, Hanson IM et al. 2020. Recurrent heterozygous PAX6 missense variants cause severe bilateral microphthalmia via predictable effects on DNA-protein interaction. Genet. Med. 22:598–609
    [Google Scholar]
  128. 128.
    Wishner BC, Ward KB, Lattman EE, Love WE. 1975. Crystal structure of sickle-cell deoxyhemoglobin at 5 Å resolution. J. Mol. Biol. 98:179–94
    [Google Scholar]
  129. 129.
    Wright CF, Fitzgerald TW, Jones WD, Clayton S, McRae JF et al. 2015. Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data. Lancet 385:1305–14
    [Google Scholar]
  130. 130.
    Yadav RP, Gakhar L, Yu L, Artemyev NO 2017. Unique structural features of the AIPL1-FKBP domain that support prenyl lipid binding and underlie protein malfunction in blindness. PNAS 114:E6536–45
    [Google Scholar]
  131. 131.
    Yang T, Ta TA, Pessah IN, Allen PD. 2003. Functional defects in six ryanodine receptor isoform-1 (RyR1) mutations associated with malignant hyperthermia and their impact on skeletal excitation-contraction coupling. J. Biol. Chem. 278:25722–30
    [Google Scholar]
  132. 132.
    Yang Y-Q, Gharibeh L, Li R-G, Xin Y-F, Wang J et al. 2013. GATA4 loss-of-function mutations underlie familial tetralogy of Fallot. Hum. Mutat. 34:1662–71
    [Google Scholar]
  133. 133.
    Yarden Y, Sliwkowski MX. 2001. Untangling the ErbB signalling network. Nat. Rev. Mol. Cell Biol. 2:127–37
    [Google Scholar]
  134. 134.
    Yates CM, Sternberg MJE. 2013. The effects of non-synonymous single nucleotide polymorphisms (nsSNPs) on protein-protein interactions. J. Mol. Biol. 425:3949–63
    [Google Scholar]
  135. 135.
    Yue P, Li Z, Moult J. 2005. Loss of protein structure stability as a major causative factor in monogenic disease. J. Mol. Biol. 353:459–73
    [Google Scholar]
  136. 136.
    Zhu G, Xie J, Kong W, Xie J, Li Y et al. 2020. Phase separation of disease-associated SHP2 mutants underlies MAPK hyperactivation. Cell 183:490–502.e18
    [Google Scholar]
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