Skip to main content

Advertisement

Log in

Discovery of mutations for Mendelian disorders

  • Review
  • Published:
Human Genetics Aims and scope Submit manuscript

Abstract

Mendelian mutations are the most medically actionable variants in the human genome and have always played a central role in its functional annotation. Despite the relative ease with which Mendelian mutations are identified compared to other classes of variants, the pace of their discovery has until recently been slow. However, recent technological advances in genomic sequencing have made the prospect of identifying all genes that can harbor Mendelian mutations an achievable near-term goal. The many lessons learned from previous discoveries of Mendelian mutations should inform future studies as I will discuss in this review. Also discussed are some of the challenges that will gain more prominence as we approach the last phase of the effort to map all Mendelian genes.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1

Similar content being viewed by others

References

  • Alazami AM, Alzahrani F, Bohlega S, Alkuraya FS (2014) SET binding factor 1 (SBF1) mutation causes Charcot-Marie-Tooth disease type 4B3. Neurology 82:1665–1666

    Article  PubMed  Google Scholar 

  • Alazami AM, Patel N, Shamseldin HE, Anazi S, Al-Dosari MS, Alzahrani F, Hijazi H, Alshammari M, Aldahmesh MA, Salih MA (2015) Accelerating novel candidate gene discovery in neurogenetic disorders via whole-exome sequencing of prescreened multiplex consanguineous families. Cell reports 10:148–161

    Article  CAS  PubMed  Google Scholar 

  • Albers CA, Paul DS, Schulze H, Freson K, Stephens JC, Smethurst PA, Jolley JD, Cvejic A, Kostadima M, Bertone P (2012) Compound inheritance of a low-frequency regulatory SNP and a rare null mutation in exon-junction complex subunit RBM8A causes TAR syndrome. Nat Genet 44:435–439

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aldahmesh MA, Khan AO, Mohamed J, Alkuraya FS (2011a) Novel recessive BFSP2 and PITX3 mutations: insights into mutational mechanisms from consanguineous populations. Genet Med 13:978–981

    Article  CAS  PubMed  Google Scholar 

  • Aldahmesh MA, Mohamed JY, Alkuraya HS, Verma IC, Puri RD, Alaiya AA, Rizzo WB, Alkuraya FS (2011b) Recessive mutations in ELOVL4 cause ichthyosis, intellectual disability, and spastic quadriplegia. Am J Hum Genet 89:745–750

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Aldahmesh MA, Khan AO, Alkuraya H, Adly N, Anazi S, Al-Saleh AA, Mohamed JY, Hijazi H, Prabakaran S, Tacke M (2013) Mutations in LRPAP1 are associated with severe myopia in humans. Am J Hum Genet 93:313–320

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Alkuraya FS (2012) Discovery of rare homozygous mutations from studies of consanguineous pedigrees. Curr Protoc Hum Genet: 6.12. 1–6.12. 13

  • Alkuraya FS (2013) The application of next-generation sequencing in the autozygosity mapping of human recessive diseases. Hum Genet 132:1197–1211

    Article  CAS  PubMed  Google Scholar 

  • Alkuraya FS (2015) Human knockout research: new horizons and opportunities. Trends Genet 31:108–115

    Article  CAS  PubMed  Google Scholar 

  • Alsalem AB, Halees AS, Anazi S, Alshamekh S, Alkuraya FS (2013) Autozygome sequencing expands the horizon of human knockout research and provides novel insights into human phenotypic variation. PLoS Genet 9:e1004030

    Article  PubMed  PubMed Central  Google Scholar 

  • Al-Salem A, Alshammari MJ, Hassan H, Alazami AM, Alkuraya FS (2013) Weaver syndrome and defective cortical development: a rare association. Am J Med Genet Part A 161:225–227

    Article  Google Scholar 

  • Anazi S, Al-Sabban E, Alkuraya F (2014) Gonadal mosaicism as a rare cause of autosomal recessive inheritance. Clin Genet 85:278–281

    Article  CAS  PubMed  Google Scholar 

  • Antonarakis SE, Beckmann JS (2006) Mendelian disorders deserve more attention. Nat Rev Genet 7:277–282

    Article  CAS  PubMed  Google Scholar 

  • Antonarakis SE, Chakravarti A, Cohen JC, Hardy J (2010) Mendelian disorders and multifactorial traits: the big divide or one for all? Nat Rev Genet 11:380–384

    Article  CAS  PubMed  Google Scholar 

  • Bohlega S, Alazami A, Cupler E, Al-Hindi H, Ibrahim E, Alkuraya F (2011) A novel syndromic form of sensory-motor polyneuropathy is linked to chromosome 22q13. 31–q13. 33. Clin Genet 79:193–195

    Article  CAS  PubMed  Google Scholar 

  • Brinkman RR, Dubé M-P, Rouleau GA, Orr AC, Samuels ME (2006) Human monogenic disorders—a source of novel drug targets. Nat Rev Genet 7:249–260

    Article  CAS  PubMed  Google Scholar 

  • Bühling F, Kouadio M, Chwieralski CE, Kern U, Hohlfeld JM, Klemm N, Friedrichs N, Roth W, Deussing JM, Peters C (2011) Gene targeting of the cysteine peptidase cathepsin H impairs lung surfactant in mice. PLoS One 6(10):e26247

    Article  PubMed  PubMed Central  Google Scholar 

  • Campbell IM, Gambin T, Jhangiani SN, Grove ML, Veeraraghavan N, Muzny DM, Shaw CA, Gibbs RA, Boerwinkle E, Yu F (2015) Multiallelic positions in the human genome: challenges for genetic analyses. Hum Mutat 37(3):231–234

    Article  PubMed  Google Scholar 

  • Chong JX, Yu J-H, Lorentzen P, Park KM, Jamal SM, Tabor HK, Rauch A, Saenz MS, Boltshauser E, Patterson KE, Nickerson DA, Bamshad MJ (2015) Gene discovery for Mendelian conditions via social networking: de novo variants in KDM1A cause developmental delay and distinctive facial features. Genet Med. doi:10.1038/gim.2015.161

    PubMed  Google Scholar 

  • Cirulli ET, Goldstein DB (2010) Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat Rev Genet 11:415–425

    Article  CAS  PubMed  Google Scholar 

  • Elsea SH, Lucas RE (2002) The mousetrap: what we can learn when the mouse model does not mimic the human disease. ILAR J 43:66–79

    Article  CAS  PubMed  Google Scholar 

  • Gai X, Ghezzi D, Johnson MA, Biagosch CA, Shamseldin HE, Haack TB, Reyes A, Tsukikawa M, Sheldon CA, Srinivasan S (2013) Mutations in FBXL4, encoding a mitochondrial protein, cause early-onset mitochondrial encephalomyopathy. Am J Hum Genet 93:482–495

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gilissen C, Hehir-Kwa JY, Thung DT, van de Vorst M, van Bon BW, Willemsen MH, Kwint M, Janssen IM, Hoischen A, Schenck A (2014) Genome sequencing identifies major causes of severe intellectual disability. Nature 511(7509):344–347

    Article  CAS  PubMed  Google Scholar 

  • Group SM (2015) Comprehensive gene panels provide advantages over clinical exome sequencing for Mendelian diseases. Genome Biol 16:134

    Article  Google Scholar 

  • Hafner C, van Oers JM, Vogt T, Landthaler M, Stoehr R, Blaszyk H, Hofstaedter F, Zwarthoff EC, Hartmann A (2006) Mosaicism of activatingFGFR3 mutations in human skin causes epidermal nevi. J Clin Investig 116:2201

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huisman SA, Redeker EJ, Maas SM, Mannens MM, Hennekam RC (2013) High rate of mosaicism in individuals with Cornelia de Lange syndrome. J Med Genet 50:339–344

    Article  CAS  PubMed  Google Scholar 

  • Indjeian VB, Kingman GA, Jones FC, Guenther CA, Grimwood J, Schmutz J, Myers RM, Kingsley DM (2016) Evolving new skeletal traits by cis-regulatory changes in bone morphogenetic proteins. Cell 164(1–2):45–56

    Article  CAS  PubMed  Google Scholar 

  • Jamuar SS, Lam A-TN, Kircher M, D’Gama AM, Wang J, Barry BJ, Zhang X, Hill RS, Partlow JN, Rozzo A (2014) Somatic mutations in cerebral cortical malformations. N Engl J Med 371:733–743

    Article  PubMed  PubMed Central  Google Scholar 

  • Jordan DM, Frangakis SG, Golzio C, Cassa CA, Kurtzberg J, Davis EE, Sunyaev SR, Katsanis N (2015) Identification of cis-suppression of human disease mutations by comparative genomics. Nature 524:225–229

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim J-I, Ju YS, Park H, Kim S, Lee S, Yi J-H, Mudge J, Miller NA, Hong D, Bell CJ (2009) A highly annotated whole-genome sequence of a Korean individual. Nature 460:1011–1015

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kong A, Frigge ML, Masson G, Besenbacher S, Sulem P, Magnusson G, Gudjonsson SA, Sigurdsson A, Jonasdottir A, Jonasdottir A (2012) Rate of de novo mutations and the importance of father/’s age to disease risk. Nature 488:471–475

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lambertson KF, Damiani SA, Might M, Shelton R, Terry SF (2015) Participant-driven matchmaking in the genomic era. Hum Mutat 36:965–973

    Article  PubMed  Google Scholar 

  • Lupski JR (2013) Genome mosaicism-one human, multiple genomes. Science 341:358–359

    Article  CAS  PubMed  Google Scholar 

  • Lupski JR, Reid JG, Gonzaga-Jauregui C, Rio Deiros D, Chen DC, Nazareth L, Bainbridge M, Dinh H, Jing C, Wheeler DA (2010) Whole-genome sequencing in a patient with Charcot–Marie–Tooth neuropathy. N Engl J Med 362:1181–1191

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • MacArthur D, Manolio T, Dimmock D, Rehm H, Shendure J, Abecasis G, Adams D, Altman R, Antonarakis S, Ashley E (2014) Guidelines for investigating causality of sequence variants in human disease. Nature 508:469–476

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marotta CA, Wilson JT, Forget BG, Weissman SM (1977) Human beta-globin messenger RNA. III. Nucleotide sequences derived from complementary DNA. J Biol Chem 252:5040–5053

    CAS  PubMed  Google Scholar 

  • Might M, Wilsey M (2014) The shifting model in clinical diagnostics: how next-generation sequencing and families are altering the way rare diseases are discovered, studied, and treated. Genet Med 16(10):736–737

    Article  CAS  PubMed  Google Scholar 

  • Nakhro K, Park J-M, Hong YB, Park JH, Nam SH, Yoon BR, Yoo JH, Koo H, Jung S-C, Kim H-L (2013) SET binding factor 1 (SBF1) mutation causes Charcot-Marie-Tooth disease type 4B3. Neurology 81:165–173

    Article  CAS  PubMed  Google Scholar 

  • Pauling L, Itano HA, Singer SJ, Wells IC (1949) Sickle cell anemia, a molecular disease. Science 110:543–548

    Article  CAS  PubMed  Google Scholar 

  • Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, Brudno M, Brunner HG, Buske OJ, Carey K, Doll C (2015) The matchmaker exchange: a platform for rare disease gene discovery. Hum Mutat 36:915–921

    Article  PubMed  Google Scholar 

  • Ronchi D, Di Fonzo A, Lin W, Bordoni A, Liu C, Fassone E, Pagliarani S, Rizzuti M, Zheng L, Filosto M (2013) Mutations in DNA2 link progressive myopathy to mitochondrial DNA instability. Am J Hum Genet 92:293–300

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sewairi W, Assiri A, Patel N, Alhashem A, Alkuraya FS (2016) Distal acroosteolysis, poikiloderma and joint stiffness: a novel laminopathy&quest. Eur J Hum Genet

  • Shaheen R, Alazami AM, Alshammari MJ, Faqeih E, Alhashmi N, Mousa N, Alsinani A, Ansari S, Alzahrani F, Al-Owain M (2012) Study of autosomal recessive osteogenesis imperfecta in Arabia reveals a novel locus defined by TMEM38B mutation. J Med Genet 49:630–635

    Article  CAS  PubMed  Google Scholar 

  • Shaheen R, Aglan M, Keppler-Noreuil K, Faqeih E, Ansari S, Horton K, Ashour A, Zaki MS, Al-Zahrani F, Cueto-González AM (2013a) Mutations in EOGT confirm the genetic heterogeneity of autosomal-recessive Adams-Oliver syndrome. Am J Hum Genet 92:598–604

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shaheen R, Ansari S, Alshammari MJ, Alkhalidi H, Alrukban H, Eyaid W, Alkuraya FS (2013b) A novel syndrome of hypohidrosis and intellectual disability is linked to COG6 deficiency. J Med Genet 50:431–436

    Article  CAS  PubMed  Google Scholar 

  • Shaheen R, Faqeih E, Ansari S, Abdel-Salam G, Al-Hassnan ZN, Al-Shidi T, Alomar R, Sogaty S, Alkuraya FS (2014a) Genomic analysis of primordial dwarfism reveals novel disease genes. Genome Res 24:291–299

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shaheen R, Rahbeeni Z, Alhashem A, Faqeih E, Zhao Q, Xiong Y, Almoisheer A, Al-Qattan SM, Almadani HA, Al-Onazi N (2014b) Neu-Laxova syndrome, an inborn error of serine metabolism, is caused by mutations in PHGDH. Am J Hum Genet 94:898–904

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shaheen R, Patel N, Shamseldin H, Alzahrani F, Al-Yamany R, Al A, Ewida N, Anazi S, Alnemer M, Elsheikh M, Alfaleh K, Alshammari M, Alhashem A, Alangari AA, Salih MA, Kircher M, Daza RM, Ibrahim N, Wakil SM, Alaqeel A, Altowaijri I, Shendure J, Al-Habib A, Faqieh E, Alkuraya FS (2015) Accelerating matchmaking of novel dysmorphology syndromes through clinical and genomic characterization of a large cohort. Genet Med. doi:10.1038/gim.2015.147

    Google Scholar 

  • Shamseldin HE, Alshammari M, Al-Sheddi T, Salih MA, Alkhalidi H, Kentab A, Repetto GM, Hashem M, Alkuraya FS (2012a) Genomic analysis of mitochondrial diseases in a consanguineous population reveals novel candidate disease genes. J Med Genet 49:234–241

    Article  PubMed  Google Scholar 

  • Shamseldin HE, Swaid A, Alkuraya FS (2012b) Lifting the lid on unborn lethal Mendelian phenotypes through exome sequencing. Genet Med 15:307–309

    Article  PubMed  PubMed Central  Google Scholar 

  • Shamseldin H, Alazami AM, Manning M, Hashem A, Caluseiu O, Tabarki B, Esplin E, Schelley S, Innes AM, Parboosingh JS (2015a) RTTN mutations cause primary microcephaly and primordial Dwarfism in humans. Am J Hum Genet 97:862–868

    Article  CAS  PubMed  Google Scholar 

  • Shamseldin HE, Tulbah M, Kurdi W, Nemer M, Alsahan N, Al Mardawi E, Khalifa O, Hashem A, Kurdi A, Babay Z (2015b) Identification of embryonic lethal genes in humans by autozygosity mapping and exome sequencing in consanguineous families. Genome Biol 16:116

    Article  PubMed  PubMed Central  Google Scholar 

  • Shamseldin HE, Faqeih E, Alasmari A, Zaki MS, Gleeson JG, Alkuraya FS (2015b) Mutations in UNC80, Encoding Part of the UNC79-UNC80-NALCN Channel Complex, Cause Autosomal-Recessive Severe Infantile Encephalopathy. Am J Hum Genet

  • Shamseldin HE, Bennett AH, Alfadhel M, Gupta V, Alkuraya FS (2016) GOLGA2, encoding a master regulator of golgi apparatus, is mutated in a patient with a neuromuscular disorder. Hum Genet 135:245–251

    Article  CAS  PubMed  Google Scholar 

  • Sobreira N, Schiettecatte F, Valle D, Hamosh A (2015) GeneMatcher: a matching tool for connecting investigators with an interest in the same gene. Hum Mutat 36:928–930

    Article  PubMed  PubMed Central  Google Scholar 

  • Veltman JA, Brunner HG (2012) De novo mutations in human genetic disease. Nat Rev Genet 13:565–575

    Article  CAS  PubMed  Google Scholar 

  • Vissers LE, de Ligt J, Gilissen C, Janssen I, Steehouwer M, de Vries P, van Lier B, Arts P, Wieskamp N, del Rosario M (2010) A de novo paradigm for mental retardation. Nat Genet 42:1109–1112

    Article  CAS  PubMed  Google Scholar 

  • Wieczorek D, Newman WG, Wieland T, Berulava T, Kaffe M, Falkenstein D, Beetz C, Graf E, Schwarzmayr T, Douzgou S (2014) Compound heterozygosity of low-frequency promoter deletions and rare loss-of-function mutations in TXNL4A causes Burn-McKeown syndrome. Am J Hum Genet 95:698–707

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yavarna T, Al-Dewik N, Al-Mureikhi M, Ali R, Al-Mesaifri F, Mahmoud L, Shahbeck N, Lakhani S, AlMulla M, Nawaz Z (2015) High diagnostic yield of clinical exome sequencing in Middle Eastern patients with Mendelian disorders. Hum Genet 134:967–980

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

I thank Ranad Shaheen and Hanan E Shamseldin for their critical review of this manuscript. FSA was supported by a grant from King Salman Center for Disability Research and a grant from King Abdulaziz City for Science and Technology (13-BIO1113-20).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Fowzan S. Alkuraya.

Ethics declarations

Conflict of interest

The author declares no conflict of interest.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Alkuraya, F.S. Discovery of mutations for Mendelian disorders. Hum Genet 135, 615–623 (2016). https://doi.org/10.1007/s00439-016-1664-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00439-016-1664-8

Keywords

Navigation