An Abnormal Splice Donor Site in One Allele of the Thyroid Peroxidase Gene in FRTL5 Rat Thyroid Cells Introduces a Premature Stop Codon: Association with the Absence of Functional Enzymatic Activity

In a screen for genes expressed specifically in gastric mucous neck cells, we identified GKN3, the recently discovered third member of the gastrokine family. We present confirmatory mouse data and novel porcine data showing that mouse GKN3 expression is confined to mucous cells of the corpus neck and antrum base and is prominently expressed in metaplastic lesions. GKN3 was proposed originally to be expressed in some human populations and a pseudogene in others. To investigate that hypothesis, we studied human GKN3 evolution in the context of its paralogous genomic neighbors, GKN1 and GKN2. Haplotype analysis revealed that GKN3 mimics GKN2 in patterns of exonic SNP allocation, whereas GKN1 appeared to be more stringently selected. GKN3 showed signatures of both directional selection and population based selective sweeps in humans. One such selective sweep includes SNP rs10187256, originally identified as an ancestral tryptophan to premature STOP codon mutation. The derived (nonancestral) allele went to fixation in Asia. We show that another SNP, rs75578132, identified 5 bp downstream of rs10187256, exhibits a second selective sweep in almost all Europeans, some Latinos, and some Africans, possibly resulting from a reintroduction of European genes during African colonization. Finally, we identify a mutation that would destroy the splice donor site in the putative exon3-intron3 boundary, which occurs in all human genomes examined to date. Our results highlight a stomach-specific human genetic locus, which has undergone various selective sweeps across European, Asian, and African populations and thus reflects geographic and ethnic patterns in genome evolution.

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Complete androgen insensitivity caused by a splice donor site mutation in intron 2 of the human androgen receptor gene resulting in an exon 2-lacking transcript with premature stop-codon and reduced expression

The Journal of Steroid Biochemistry and Molecular Biology ◽

10.1016/s0960-0760(98)00157-5 ◽

1999 ◽

Vol 68 (1-2) ◽

pp. 1-9 ◽

Cited By ~ 17

Author(s):

Olaf José-Carlos Hellwinkel ◽

Kerstin Bull ◽

Paul-Martin Holterhus ◽

Nicole Homburg ◽

Dagmar Struve ◽

...

Keyword(s):

Stop Codon ◽

Receptor Gene ◽

Donor Site ◽

Premature Stop Codon ◽

Androgen Receptor Gene ◽

Splice Donor Site ◽

Site Mutation ◽

Exon 2 ◽

Human Androgen Receptor Gene ◽

Splice Donor Site Mutation

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Sterol Regulatory Element-Binding Proteins Are Regulators of the Rat Thyroid Peroxidase Gene in Thyroid Cells

PLoS ONE ◽

10.1371/journal.pone.0091265 ◽

2014 ◽

Vol 9 (3) ◽

pp. e91265 ◽

Cited By ~ 6

Author(s):

Christine Rauer ◽

Robert Ringseis ◽

Susanne Rothe ◽

Gaiping Wen ◽

Klaus Eder

Keyword(s):

Binding Proteins ◽

Regulatory Element ◽

Thyroid Peroxidase ◽

Thyroid Cells ◽

Peroxidase Gene ◽

Sterol Regulatory Element ◽

Rat Thyroid

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Metastatic Follicular Thyroid Carcinoma Arising from Congenital Goiter as a Result of a Novel Splice Donor Site Mutation in the Thyroglobulin Gene

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/jc.2005-2302 ◽

2006 ◽

Vol 91 (3) ◽

pp. 740-746 ◽

Cited By ~ 30

Author(s):

Ali S. Alzahrani ◽

Essa Y. Baitei ◽

Minjing Zou ◽

Yufei Shi

Keyword(s):

Thyroid Carcinoma ◽

Malignant Transformation ◽

Follicular Thyroid Carcinoma ◽

Donor Site ◽

Premature Stop Codon ◽

Pcr Amplification ◽

Splice Donor Site ◽

Rt Pcr ◽

Cdna Fragment ◽

Splice Donor

Abstract Context: Defects in thyroglobulin (Tg) synthesis are one of the causes of thyroid dyshormonogenesis. Only a few mutations in the Tg gene have been described. Objectives: We describe a novel Tg gene mutation and discuss the mechanisms by which it causes dyshormonogenesis with subsequent malignant transformation. Cases: Two siblings aged 21 and 19 yr presented with recurrent goiters for which they had undergone multiple thyroid surgeries since early childhood. The older sibling was diagnosed with metastatic follicular thyroid carcinoma at age 15 yr. Methods: The entire coding region and intron-exon boundaries of the Tg gene were amplified and sequenced from the patients. We also sequenced the boundaries of exon 5 and intron 5 from both parents. RT-PCR amplification of a cDNA fragment encompassing exons 4–6 was also performed. Results: A homozygous G to A point mutation at position +1 of the splice donor site of intron 5 (g.IVS5+1G→A) was detected in both patients, whereas a monoallelic mutation was found in their parents. RT-PCR amplification of a cDNA fragment covering exons 4–6 revealed a 191-bp fragment in the patients and 351- and 191-bp fragments in the parents. Sequence analysis of these two fragments confirmed deletion of exon 5 in the 191-bp fragment. Conclusions: Aberrant splicing occurred as a result of the g.IVS5+1G→A mutation, which caused fusion of exons 4 and 6, resulting in the frame shift at codon position 141 and a premature stop codon at position 147 (FS141→147X). The malignant transformation is likely a result of prolonged TSH stimulation.

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O.J.C. Hellwinkel, K. Bull, P.M. Holterhus, N. Homberg, D. Struve, O. Hiort. Complete androgen insensitivity caused by a splice donor site mutation in intron 2 of the human androgen receptor gene resulting in an exon 2-lacking transcript with premature stop-codon and reduced expression. Journal of Steroid Biochemistry and Molecular Biology Vol 68 (1999) 1–9

The Journal of Steroid Biochemistry and Molecular Biology ◽

10.1016/s0960-0760(99)00098-9 ◽

1999 ◽

Vol 71 (1-2) ◽

pp. 91 ◽

Cited By ~ 1

Keyword(s):

Stop Codon ◽

Receptor Gene ◽

Donor Site ◽

Premature Stop Codon ◽

Androgen Receptor Gene ◽

Splice Donor Site ◽

Site Mutation ◽

Exon 2 ◽

Human Androgen Receptor Gene ◽

Splice Donor Site Mutation

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Biallelic variants in COPB1 cause a novel, severe intellectual disability syndrome with cataracts and variable microcephaly

Genome Medicine ◽

10.1186/s13073-021-00850-w ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

William L. Macken ◽

Annie Godwin ◽

Gabrielle Wheway ◽

Karen Stals ◽

Liliya Nazlamova ◽

...

Keyword(s):

Genome Sequencing ◽

Donor Site ◽

Xenopus Tropicalis ◽

Splice Donor Site ◽

Homologous Region ◽

Disease Genes ◽

Coat Proteins ◽

Splice Donor ◽

Severe Intellectual Disability

Abstract Background Coat protein complex 1 (COPI) is integral in the sorting and retrograde trafficking of proteins and lipids from the Golgi apparatus to the endoplasmic reticulum (ER). In recent years, coat proteins have been implicated in human diseases known collectively as “coatopathies”. Methods Whole exome or genome sequencing of two families with a neuro-developmental syndrome, variable microcephaly and cataracts revealed biallelic variants in COPB1, which encodes the beta-subunit of COPI (β-COP). To investigate Family 1’s splice donor site variant, we undertook patient blood RNA studies and CRISPR/Cas9 modelling of this variant in a homologous region of the Xenopus tropicalis genome. To investigate Family 2’s missense variant, we studied cellular phenotypes of human retinal epithelium and embryonic kidney cell lines transfected with a COPB1 expression vector into which we had introduced Family 2’s mutation. Results We present a new recessive coatopathy typified by severe developmental delay and cataracts and variable microcephaly. A homozygous splice donor site variant in Family 1 results in two aberrant transcripts, one of which causes skipping of exon 8 in COPB1 pre-mRNA, and a 36 amino acid in-frame deletion, resulting in the loss of a motif at a small interaction interface between β-COP and β’-COP. Xenopus tropicalis animals with a homologous mutation, introduced by CRISPR/Cas9 genome editing, recapitulate features of the human syndrome including microcephaly and cataracts. In vitro modelling of the COPB1 c.1651T>G p.Phe551Val variant in Family 2 identifies defective Golgi to ER recycling of this mutant β-COP, with the mutant protein being retarded in the Golgi. Conclusions This adds to the growing body of evidence that COPI subunits are essential in brain development and human health and underlines the utility of exome and genome sequencing coupled with Xenopus tropicalis CRISPR/Cas modelling for the identification and characterisation of novel rare disease genes.

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A rare large duplication of MLH1 identified in Lynch syndrome

Hereditary Cancer in Clinical Practice ◽

10.1186/s13053-021-00167-0 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Abhishek Kumar ◽

Nagarajan Paramasivam ◽

Obul Reddy Bandapalli ◽

Matthias Schlesner ◽

Tianhui Chen ◽

...

Keyword(s):

Amino Acid ◽

Lynch Syndrome ◽

Splice Site ◽

Stop Codon ◽

Premature Stop Codon ◽

Splice Donor Site ◽

Laboratory Diagnostics ◽

Mmr Genes ◽

Base Pair Deletion ◽

Splice Site Variant

Abstract Background The most frequently identified strong cancer predisposition mutations for colorectal cancer (CRC) are those in the mismatch repair (MMR) genes in Lynch syndrome. Laboratory diagnostics include testing tumors for immunohistochemical staining (IHC) of the Lynch syndrome-associated DNA MMR proteins and/or for microsatellite instability (MSI) followed by sequencing or other techniques, such as denaturing high performance liquid chromatography (DHPLC), to identify the mutation. Methods In an ongoing project focusing on finding Mendelian cancer syndromes we applied whole-exome/whole-genome sequencing (WES/WGS) to 19 CRC families. Results Three families were identified with a pathogenic/likely pathogenic germline variant in a MMR gene that had previously tested negative in DHPLC gene variant screening. All families had a history of CRC in several family members across multiple generations. Tumor analysis showed loss of the MMR protein IHC staining corresponding to the mutated genes, as well as MSI. In family A, a structural variant, a duplication of exons 4 to 13, was identified in MLH1. The duplication was predicted to lead to a frameshift at amino acid 520 and a premature stop codon at amino acid 539. In family B, a 1 base pair deletion was found in MLH1, resulting in a frameshift and a stop codon at amino acid 491. In family C, we identified a splice site variant in MSH2, which was predicted to lead loss of a splice donor site. Conclusions We identified altogether three pathogenic/likely pathogenic variants in the MMR genes in three of the 19 sequenced families. The MLH1 variants, a duplication of exons 4 to 13 and a frameshift variant, were novel, based on the InSiGHT and ClinVar databases; the MSH2 splice site variant was reported by a single submitter in ClinVar. As a variant class, duplications have rarely been reported in the MMR gene literature, particularly those covering several exons.

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A 5′ splice site mutation affecting the pre-mRNA splicing of two upstream exons in the collagen COL1A1 gene. Exon 8 skipping and altered definition of exon 7 generates truncated proα1(I) chains with a non-collagenous insertion destabilizing the triple helix

Biochemical Journal ◽

10.1042/bj3020729 ◽

1994 ◽

Vol 302 (3) ◽

pp. 729-735 ◽

Cited By ~ 21

Author(s):

J F Bateman ◽

D Chan ◽

I Moeller ◽

M Hannagan ◽

W G Cole

Keyword(s):

Splice Site ◽

De Novo ◽

Donor Site ◽

Mrna Splicing ◽

Splice Donor Site ◽

Sequence Motif ◽

Type I ◽

Splice Donor ◽

Site Mutation ◽

Definition Of

A heterozygous de novo G to A point mutation in intron 8 at the +5 position of the splice donor site of the gene for the pro alpha 1(I) chain of type I procollagen, COL1A1, was defined in a patient with type IV osteogenesis imperfecta. The splice donor site mutation resulted not only in the skipping of the upstream exon 8 but also unexpectedly had the secondary effect of activating a cryptic splice site in the next upstream intron, intron 7, leading to re-definition of the 3′ limit of exon 7. These pre-mRNA splicing aberrations cause the deletion of exon 8 sequences from the mature mRNA and the inclusion of 96 bp of intron 7 sequence. Since the mis-splicing of the mutant allele product resulted in the maintenance of the correct codon reading frame, the resultant pro alpha 1(I) chain contained a short non-collagenous 32-amino-acid sequence insertion within the repetitive Gly-Xaa-Yaa collagen sequence motif. At the protein level, the mutant alpha 1(I) chain was revealed by digestion with pepsin, which cleaved the mutant procollagen within the protease-sensitive non-collagenous insertion, producing a truncated alpha 1(I). This protease sensitivity demonstrated the structural distortion to the helical structure caused by the insertion. In long-term culture with ascorbic acid, which stimulates the formation of a mature crosslinked collagen matrix, and in tissues, there was no evidence of the mutant chain, suggesting that during matrix formation the mutant chain was unable to stably incorporated into the matrix and was degraded proteolytically.

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