Mandibulofacial Dysostosis Attributed to a Recessive Mutation of CYP26C1 in Hereford Cattle

In spring 2020, six Hereford calves presented with congenital facial deformities attributed to a condition we termed mandibulofacial dysostosis (MD). Affected calves shared hallmark features of a variably shortened and/or asymmetric lower mandible and bilateral skin tags present 2–10 cm caudal to the commissure of the lips. Pedigree analysis revealed a single common ancestor shared by the sire and dam of each affected calf. Whole-genome sequencing (WGS) of 20 animals led to the discovery of a variant (Chr26 g. 14404993T>C) in Exon 3 of CYP26C1 associated with MD. This missense mutation (p.L188P), is located in an α helix of the protein, which the identified amino acid substitution is predicted to break. The implication of this mutation was further validated through genotyping 2 additional affected calves, 760 other Herefords, and by evaluation of available WGS data from over 2500 other individuals. Only the affected individuals were homozygous for the variant and all heterozygotes had at least one pedigree tie to the suspect founder. CYP26C1 plays a vital role in tissue-specific regulation of retinoic acid (RA) during embryonic development. Dysregulation of RA can result in teratogenesis by altering the endothelin-1 signaling pathway affecting the expression of Dlx genes, critical to mandibulofacial development. We postulate that this recessive missense mutation in CYP26C1 impacts the catalytic activity of the encoded enzyme, leading to excess RA resulting in the observed MD phenotype.

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17 A De novo Recessive Mutation Causative of Mandibulofacial Dysostosis in Hereford Cattle

Journal of Animal Science ◽

10.1093/jas/skab054.047 ◽

2021 ◽

Vol 99 (Supplement_1) ◽

pp. 27-27

Author(s):

Renae L Sieck ◽

Anna M Fuller ◽

Patrick Bedwell ◽

Jack Ward ◽

Stacy Sanders ◽

...

Keyword(s):

Retinoic Acid ◽

Missense Mutation ◽

De Novo ◽

Pedigree Analysis ◽

De Novo Mutation ◽

Recessive Mutation ◽

Hereford Cattle ◽

Specific Regulation ◽

Mandibulofacial Dysostosis ◽

Mode Of Inheritance

Abstract In spring 2020, six Hereford calves presented with congenital craniofacial abnormalities attributed to a condition we termed mandibulofacial dysostosis (MD). Pedigree analysis revealed a single common ancestor shared by the sire and dam of each affected calf. We hypothesized that MD in Hereford cattle is attributed to a de novo mutation with an autosomal recessive mode of inheritance. To avoid production of affected calves, the objective of this study was to identify the cause of MD. Whole-genome sequencing (WGS) of 20 animals (3 affected, 7 obligate carriers, 10 related) yielded 143 variants matching the hypothesized mode of inheritance. Genotyping of 2 additional affected calves, 760 Herefords, and evaluation of WGS data from over 2,500 other individuals led to the discovery of a missense mutation (Chr26 g. 14404993 T >C) in CYP26C1 associated with MD. The amino acid change due to the CYP26C1 variant (p. L188P) is located in an α helix of the protein; modeling suggests the substitution breaks the helix. The mutation is predicted to be deleterious (SIFT = 0) and is otherwise conserved across species. In our data, all heterozygotes had at least one pedigree tie to the suspect founder. CYP26C1 plays a vital role in tissue-specific regulation of retinoic acid (RA) during embryonic development. Dysregulation of RA can result in teratogenesis by altering the endothelin-1 signaling pathway affecting the expression of Dlx genes, critical to mandibulofacial development. Further, multiple human conditions with similar pathologic characteristics are attributed to dysfunction of this gene and/or retinoic acid signaling. We conclude that this recessive missense mutation in CYP26C1 impacts the catalytic activity of the encoded enzyme, leading to excess RA and resulting in the MD phenotype. Breeders can now genotype their animals to identify carriers. These data also contribute to expanding the understanding of craniofacial development across species.

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Identification of a compound heterozygote in LYST gene: a case report on Chediak-Higashi syndrome

BMC Medical Genetics ◽

10.1186/s12881-019-0922-8 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Yinsen Song ◽

Zhengping Dong ◽

Shuying Luo ◽

Junmei Yang ◽

Yuebing Lu ◽

...

Keyword(s):

Missense Mutation ◽

Genetic Diseases ◽

Amplicon Sequencing ◽

Bone Marrow Examination ◽

Pathogenic Mutation ◽

Pedigree Analysis ◽

Compound Heterozygote ◽

Loss Of Function ◽

Causative Gene ◽

Chediak Higashi Syndrome

Abstract Background Chediak-Higashi Syndrome (CHS) is a rare autosomal recessive disease caused by loss of function of the lysosomal trafficking regulator protein. The causative gene LYST/CHS1 was cloned and identified in 1996, which showed significant homology to other species such as bovine and mouse. To date, 74 pathogenic or likely pathogenic mutations had been reported. Case presentation Here we describe a compound heterozygote in LYST gene, which was identified in a 4-year-old female patient. The patient showed skin hypopigmentation, sensitivity to light, mild splenomegaly and reduction of platelets in clinical examination. Giant intracytoplasmic inclusions were observed in the bone marrow examination, suggesting the diagnosis of CHS. Amplicon sequencing was performed to detect pathogenic mutation in LYST gene. The result was confirmed by two-generation pedigree analysis base on sanger sequencing. Conclusion A compound heterozygote in LYST gene, consisting of a missense mutation c.5719A > G and an intron mutation c.4863-4G > A, was identified from the patient by using amplicon sequencing. The missense mutation is reported for the first time. Two-generation pedigree analysis showed these two mutations were inherited from the patient’s parents, respectively. Our result demonstrated that amplicon sequencing has great potential for accelerating and improving the diagnosis of rare genetic diseases.

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DMC1 mutation that causes human non-obstructive azoospermia and premature ovarian insufficiency identified by whole-exome sequencing

Journal of Medical Genetics ◽

10.1136/jmedgenet-2017-104992 ◽

2018 ◽

Vol 55 (3) ◽

pp. 198-204 ◽

Cited By ~ 24

Author(s):

Wen-Bin He ◽

Chao-Feng Tu ◽

Qiang Liu ◽

Lan-Lan Meng ◽

Shi-Min Yuan ◽

...

Keyword(s):

Exome Sequencing ◽

Missense Mutation ◽

Whole Exome Sequencing ◽

Male Patient ◽

Histological Analysis ◽

Pedigree Analysis ◽

Obstructive Azoospermia ◽

Ovarian Insufficiency ◽

Causative Gene ◽

Whole Exome

BackgroundThe genetic causes of the majority of male and female infertility caused by human non-obstructive azoospermia (NOA) and premature ovarian insufficiency (POI) with meiotic arrest are unknown.ObjectiveTo identify the genetic cause of NOA and POI in two affected members from a consanguineous Chinese family.MethodsWe performed whole-exome sequencing of DNA from both affected patients. The identified candidate causative gene was further verified by Sanger sequencing for pedigree analysis in this family. In silico analysis was performed to functionally characterise the mutation, and histological analysis was performed using the biopsied testicle sample from the male patient with NOA.ResultsWe identified a novel homozygous missense mutation (NM_007068.3: c.106G>A, p.Asp36Asn) in DMC1, which cosegregated with NOA and POI phenotypes in this family. The identified missense mutation resulted in the substitution of a conserved aspartic residue with asparaginate in the modified H3TH motif of DMC1. This substitution results in protein misfolding. Histological analysis demonstrated a lack of spermatozoa in the male patient’s seminiferous tubules. Immunohistochemistry using a testis biopsy sample from the male patient showed that spermatogenesis was blocked at the zygotene stage during meiotic prophase I.ConclusionsTo the best of our knowledge, this is the first report identifying DMC1 as the causative gene for human NOA and POI. Furthermore, our pedigree analysis shows an autosomal recessive mode of inheritance for NOA and POI caused by DMC1 in this family.

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THE TIMING OF UV MUTAGENESIS IN YEAST: A PEDIGREE ANALYSIS OF INDUCED RECESSIVE MUTATION

Genetics ◽

10.1093/genetics/87.2.237 ◽

1977 ◽

Vol 87 (2) ◽

pp. 237-248

Author(s):

A P James ◽

B J Kilbey

Keyword(s):

Dna Replication ◽

Pedigree Analysis ◽

Yeast Cells ◽

Recessive Mutation ◽

Post Irradiation ◽

Recessive Mutations ◽

Pyrimidine Dimers ◽

Irradiation Cell ◽

High Level ◽

Diploid Cells

ABSTRACT The mechanism of UV-induced mutation in eukaryotes was studied in individual yeast cells by a procedure that combined pedigree analysis and tetrad analysis. The technique involved the induction of recessive lethals and semilethals in G1 diploid cells. Induced frequencies were 25 and 61 percent at survival levels of 90 and 77 percent, respectively. No evidence of gross chromosome aberrations was detected. Recessive mutations that affect only one strand or that affect both strands of the DNA molecule are induced much at random among a population of cells, and both types can occur within the same cell. However, the data confirm that two-strand mutations are in the majority after a low level of irradiation. The simplest explanation involves a mechanism whereby most mutations are fixed in both strands prior to the first round of post-irradiation DNA replication. The recessive mutational consequences of irradiation are exhausted at the conclusion of the first post-irradiation cell division, although dominant-lethal sectoring continues at a high level through the second post-irradiation division. It is concluded that pyrimidine dimers that persist to the second round of DNA replication are rare or ineffective.

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Positional Cloning of the Mouse Scat Mutation Reveals a Critical Role for RASA3, a Ras GTPase Activating Protein, in Vertebrate Erythropoiesis.

Blood ◽

10.1182/blood.v114.22.776.776 ◽

2009 ◽

Vol 114 (22) ◽

pp. 776-776

Author(s):

Luanne L. Peters ◽

Steven L. Ciciotte ◽

E. Ricky Chan ◽

Babette Gwynn ◽

Amy J. Lambert ◽

...

Keyword(s):

Missense Mutation ◽

Positional Cloning ◽

Conflicts Of Interest ◽

Critical Role ◽

Chromosome 8 ◽

Recessive Mutation ◽

Severe Thrombocytopenia ◽

Gtpase Activating Protein ◽

Form Analysis ◽

Mild Anemia

Abstract Abstract 776 The spontaneous recessive mutation scat (severe combined anemia and thrombocytopenia) arose on the inbred BALB/cBy (BALB) mouse strain. The phenotype of scat is cyclic. All homozygotes are severely anemic and thrombocytopenic at birth. Leukocytes are also significantly depleted (Table). Approximately 13% die during this first “crisis” episode that lasts, on average, until the 9th postnatal day. Remarkably, a spontaneous remission ensues in those surviving the neonatal crisis period wherein all peripheral blood values revert to normal. A second crisis follows, and 94% of the mice die by 30 days of age. The recessive ENU (N-ethyl-N-nitrosourea)-induced mutation, hlb381, on the C57BL/6J (B6) background, is characterized by severe thrombocytopenia and leukopenia with mild anemia. Unlike scat, hlb381 is not cyclical. The phenotype is present at birth and persists throughout life. Despite the phenotypic differences, scat and hlb381 interact genetically; double heterozygotes show non-cyclical severe thrombocytopenia and leukopenia, and mild anemia (Table). This interaction implies that the scat and hlb381 genetic defects affect the same gene or distinct genes within the same pathway. Both scat and hlb381 mapped to overlapping intervals on mouse chromosome 8. Sequence analysis of genes within the interval identified Rasa3 (GAPIII, GAP1IP4BP) as a strong candidate gene for both scat and hlb381. In scat, Rasa3 carries a missense mutation near the N-terminus (G125V, exon 5) and, in hlb381, a missense mutation near the C-terminus (H794L, exon 23). RASA3 is a GTPase activating protein (GAP) that negatively regulates p21 Ras function by accelerating GTP hydrolysis and converting Ras to the inactive GDP bound form. Analysis in Panther and SIFT predicts that both residues are highly conserved and substitutions are likely to be deleterious. Rasa3 is widely expressed throughout embryonic and fetal development in mice, and is ubiquitously expressed in zebrafish 24 hours post fertilization (hpf). RASA3 protein is detected in erythroid tissues and platelets in the adult mouse. Analysis of scat spleen and bone marrow erythrocyte populations by FACS (dual staining for Ter119 and CD71 followed by forward scatter of the Ter119 high population) reveals a severe block in erythropoiesis during crisis periods. The proerythroblast, EryA (basophilic erythroblasts), and EryB (late basophilic and polychromatophilic erythroblasts) populations are significantly increased in frequency vs. wild type, and the EryC (orthochromatophilic erythroblasts and reticulocytes) population is markedly decreased. Annexin V staining revealed no significant differences in any of these populations. Notably, a similar delay in erythroid maturation, albeit much milder, is also seen in hlb381. In pull-down assays using the Ras-binding domain of Raf1 to affinity purify active GTP-bound Ras followed by detection by western blotting with pan-Ras antibody, active GTP-bound Ras is deficient in scat crisis red cells but recovers during remission. Finally, injection of two independent splice-blocking morpholinos designed to disrupt exon 5 and induce disruption of rasa3 mRNA processing resulted in a major decrease in the number of hemoglobinized cells when stained with o-dianisidine at 48 and 72 hpf in zebrafish. Over 90% of morphants showed no hemoglobinized cells at all, or vastly reduced numbers (<20) of hemoglobinized cells. We conclude that RASA3 plays a critical role in vertebrate erythropoiesis. Differences in the scat and hlb381 phenotypes likely result from allele-specific interactions mediated by the different genetic backgrounds (B6 vs. BALB) or domain-specific functions of the RASA3 protein.Hematological ValuesWBC × 103/μLRBC × 106/μLHb g/dLHct %Reticulocytes %Platelets × 103/μLSpleen weight (% body weight)BALB-scat homozygotes in crisis and remissionBALB-nl5.28.713.241.911.79550.74 scat crisis2.4*2.8*4.2*14.5*51.6*145*2.69*scat remission4.17.912.541.022.95611.22BALB,B6-hlb381 homozygotes and scat/hlb381 double heterozygotesBALB,B6-nl5.19.113.744.08.612190.28 hlb381/hlb3812.1*9.113.343.512.0*24*0.50*hlb381/scat2.4*8.4*12.3*39.9*12.1*14*NAAll mice 18-30 days old. All values X ± SD; nl, normal littermates, NA, no data available.*P < 0.05 vs. normal littermates Disclosures: No relevant conflicts of interest to declare.

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A Novel Missense Mutation p.Gly162Glu of the Gene MYL2 Involved in Hypertrophic Cardiomyopathy: A Pedigree Analysis of a Proband

Molecular Diagnosis & Therapy ◽

10.1007/s40291-018-0324-1 ◽

2018 ◽

Vol 22 (2) ◽

pp. 219-223 ◽

Cited By ~ 2

Author(s):

Pauline Renaudin ◽

Alexandre Janin ◽

Gilles Millat ◽

Philippe Chevalier

Keyword(s):

Hypertrophic Cardiomyopathy ◽

Missense Mutation ◽

Pedigree Analysis

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Pro239Ser: A Novel Recessive Mutation of the Pit-1 Gene in Seven Middle Eastern Children with Growth Hormone, Prolactin, and Thyrotropin Deficiency1

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/jcem.83.6.4901 ◽

1998 ◽

Vol 83 (6) ◽

pp. 2079-2083 ◽

Cited By ~ 1

Author(s):

Flavia Pernasetti ◽

Robert D. G. Milner ◽

Abdullah A. Z. Al Ashwal ◽

Francis de Zegher ◽

Viviana M. Chavez ◽

...

Keyword(s):

Gene Expression ◽

Growth Hormone ◽

Anterior Pituitary ◽

Middle Eastern ◽

Recessive Mutation ◽

Specific Gene ◽

Pituitary Development ◽

Domain Protein ◽

Α Helix ◽

Tsh Deficiency

Pit-1, a member of the POU-homeo domain protein family, is one of the transcription factors responsible for anterior pituitary development and pituitary-specific gene expression. Here, we describe seven children with GH, PRL, and TSH deficiency from three, reportedly unrelated, Middle Eastern families, harboring a newly recognized Pro->Ser recessive mutation in codon 239 of the Pit-1 gene. The mutated residue is located at the beginning of the second α-helix of the POU-homeodomain and is strictly conserved among all POU proteins. The Pro239Ser mutant binds DNA normally but is unable to stimulate transcription.

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A Novel Missense Mutation in TNNI3K Causes Recessively Inherited Cardiac Conduction Disease in a Consanguineous Pakistani Family

Genes ◽

10.3390/genes12081282 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1282

Author(s):

Shafaq Ramzan ◽

Stephanie Tennstedt ◽

Muhammad Tariq ◽

Sheraz Khan ◽

Hafiza Noor Ul Ayan ◽

...

Keyword(s):

Missense Mutation ◽

Troponin I ◽

Binding Pocket ◽

Kinase Domain ◽

Cardiac Conduction ◽

Recessive Mutation ◽

High Morbidity ◽

Pakistani Family ◽

Threatening Condition ◽

Dynamics Simulations

Cardiac conduction disease (CCD), which causes altered electrical impulse propagation in the heart, is a life-threatening condition with high morbidity and mortality. It exhibits genetic and clinical heterogeneity with diverse pathomechanisms, but in most cases, it disrupts the synchronous activity of impulse-generating nodes and impulse-conduction underlying the normal heartbeat. In this study, we investigated a consanguineous Pakistani family comprised of four patients with CCD. We applied whole exome sequencing (WES) and co-segregation analysis, which identified a novel homozygous missense mutation (c.1531T>C;(p.Ser511Pro)) in the highly conserved kinase domain of the cardiac troponin I-interacting kinase (TNNI3K) encoding gene. The behaviors of mutant and native TNNI3K were compared by performing all-atom long-term molecular dynamics simulations, which revealed changes at the protein surface and in the hydrogen bond network. Furthermore, intra and intermolecular interaction analyses revealed that p.Ser511Pro causes structural variation in the ATP-binding pocket and the homodimer interface. These findings suggest p.Ser511Pro to be a pathogenic variant. Our study provides insights into how the variant perturbs the TNNI3K structure-function relationship, leading to a disease state. This is the first report of a recessive mutation in TNNI3K and the first mutation in this gene identified in the Pakistani population.

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Family-based whole-exome sequencing identifies novel loss-of-function mutations of FBN1 for Marfan syndrome

PeerJ ◽

10.7717/peerj.5927 ◽

2018 ◽

Vol 6 ◽

pp. e5927 ◽

Cited By ~ 3

Author(s):

Zhening Pu ◽

Haoliang Sun ◽

Junjie Du ◽

Yue Cheng ◽

Keshuai He ◽

...

Keyword(s):

Marfan Syndrome ◽

Genetic Diagnosis ◽

Clinical Manifestations ◽

Connective Tissue Disorder ◽

Pedigree Analysis ◽

Vital Role ◽

Loss Of Function ◽

Sequencing Data ◽

Whole Exome

Background Marfan syndrome (MFS) is an inherited connective tissue disorder affecting the ocular, skeletal and cardiovascular systems. Previous studies of MFS have demonstrated the association between genetic defects and clinical manifestations. Our purpose was to investigate the role of novel genetic variants in determining MFS clinical phenotypes. Methods We sequenced the whole exome of 19 individuals derived from three Han Chinese families. The sequencing data were analyzed by a standard pipeline. Variants were further filtered against the public database and an in-house database. Then, we performed pedigree analysis under different inheritance patterns according to American College of Medical Genetics guidelines. Results were confirmed by Sanger sequencing. Results Two novel loss-of-function indels (c.5027_5028insTGTCCTCC, p.D1677Vfs*8; c.5856delG, p.S1953Lfs*27) and one nonsense variant (c.8034C>A, p.Y2678*) of FBN1 were identified in Family 1, Family 2 and Family 3, respectively. All affected members carried pathogenic mutations, whereas other unaffected family members or control individuals did not. These different kinds of loss of function (LOF) variants of FBN1 were located in the cbEGF region and a conserved domain across species and were not reported previously. Conclusions Our study extended and strengthened the vital role of FBN1 LOF mutations in the pathogenesis of MFS with an autosomal dominant inheritance pattern. We confirm that genetic testing by next-generation sequencing of blood DNA can be fundamental in helping clinicians conduct mutation-based pre- and postnatal screening, genetic diagnosis and clinical management for MFS.

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