Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Variant identification”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 829 records · Page 46Linked to original sources
PubMed2004

First report of a genetic polymorphism of the cytochrome P450 3A43 (CYP3A43) gene: identification of a loss-of-function variant.

In the present study, we report the first investigation of polymorphisms in the human CYP3A43 gene. A screening for sequence variations in the 5'-flanking and protein coding regions of the CYP3A43 gene was performed by a Polymerase Chain Reaction - Single Strand Conformational Polymorphism (PCR-SSCP) strategy, using DNA samples from 48 unrelated French individuals. Three polymorphisms in the coding region were identified, comprising two nucleotide substitutions, one silent (c.1047C>T) and one missense mutation (c.1018C>G/P340A), and a frame shift mutation (c.74delA), leading to a premature stop codon and, presumably, to a severely truncated protein. In order to evaluate the extent of the frame shift mutation in a larger population, 352 individuals were further genotyped. Thirty-four samples (4.83%) were found to be heterozygous and one homozygous (0.14%) for the nucleotide deletion, which suggests that, although the potential significance of this polymorphism remains to be further evaluated, some individuals are deficient for CYP3A43 activity.

Alleles↗
PubMed1997

Identification of mutations in a Sindbis virus variant able to establish persistent infection in BHK cells: the importance of a mutation in the nsP2 gene.

Sindbis virus is a positive strand RNA virus that has provided a valuable model for studying virus structure and replication. It is also being developed as a vector for the expression of heterologous proteins. Many studies with this virus are carried out in cultured BHK cells where infection is usually highly cytopathic and within 1 or 2 days after infection all of the cells are dead. Weiss et al. had established a persistently infected culture of BHK cells by infecting the cells with a virus preparation highly enriched in defective interfering (DI) particles and had isolated an attenuated virus, SIN-1 virus, from the culture [Weiss et al. (1980) J. Virol. 33, 463-474]. SIN-1 virus, free of DI particles, was able to establish a persistent infection in BHK cells. We initiated studies to determine what changes in the genome of the virus were responsible for this phenotype. We describe here the cDNA cloning and sequencing of the 5' terminus and the four nonstructural protein genes from SIN-1 virus. A single coding mutation in the nsP2 gene (a predicted change of Pro-726 --> Ser) produced a virus that was able to establish persistent infection in BHK cells. Additional mutations in the other genes were required to decrease the synthesis of viral RNA to a level similar to that found in cells infected with SIN-1 virus. Incorporation of the nsP2 mutation into a Sindbis virus expression vector led to a higher level of synthesis of the reporter protein, beta-galactosidase, than that obtained with the original Sindbis virus replicon.

Animals↗
PubMed2006

Identification and characterization of syntaxin 1 antisense variants in Limulus polyphemus.

1.A Limulus SMART(TM) cDNA library screening resulted in the cloning of four syntaxin 1 homologs (referred to as Limulus syntaxin [Lim-syn] 1A, 1B, 1C, and 1D) (Wang, Y., Cao, Z., Xu, W., Kemp, M. D., McAdory, B. S., Newkirk, R. F., Ivy, M. T., and Townsel, J. G. (2004). Gene 326:189-199) and two novel intron-retaining syntaxin 1-like variants, designated Limulus syntaxin variant [Lim-synV] 1A/1C and Lim-synV 1B/1D. 2.The variants exhibited high amino acid sequence identity with the four syntaxin 1 homologs. Specifically, Lim-synV 1A/1C and Lim-synV 1B/1D were homologous to Lim-syn 1A/1C and Lim-syn 1B/1D, respectively. Surprisingly, both Lim-synV 1A/1C and 1B/1D are unusual in that each has a poly A+ tail, an intron, and the common splice motif "GT-AG" at the intron-exon boundary. Exons one and two on the complementary transcript of Lim-synV 1B/1D are separated by a 150 bp intron beginning at #95/96 of the predicted sequences for Lim-syn 1B and 1D, respectively. 3. In contrast, examination of the approximately 3.17 kb Lim-synV 1A/1C clone indicated the inclusion of an insert of 1120 base pairs (bp) beginning at codon #37/38 of the predicted Lim-syn 1A and 1C cDNAs' open reading frames (ORFs). Further, the intron sequence of Lim-synV 1A/C contained multiple stop codons and showed no significant homology to other known sequences as determined by a search of the GenBank database. Thus, the focus of this paper will be Lim-synV 1B/D exclusively. 4. To substantiate that an intron is retained in the full-length mRNA, two types of syntaxin cDNA fragments for Lim-syn 1B/D were generated by RT-PCR and analyzed on Northern blots. The products generated were a mixture of intron-retaining, as well as intron-spliced products. The syntaxin-like variants that retained the intron presumably are derived from a mRNA molecule that has not undergone splicing.5. Although the significance of such intron-containing mRNAs in Limulus has not yet been elucidated, future studies of such variants may serve to broaden our knowledge concerning established splicing mechanisms as well as to focus attention on nonconventional concepts about gene product regulation.

Amino Acid Sequence↗
PubMed2026

Identification of a Novel Splice-Site variant in TACR3 (c.888 + 1G > A) Associated with Asthenozoospermia and Hypogonadotropic Hypogonadism in an Iranian Family.

BACKGROUND: TACR3 encodes the receptor for neurokinin B, a key regulator of the hypothalamic-pituitary-gonadal axis. Disruption of this pathway can impair gonadotropin release and male reproductive function. Given the genetic heterogeneity of male infertility, this study aimed to identify novel variants in TACR3 that may underlie asthenozoospermia and related hormonal abnormalities. METHODS: Fifteen infertile men with confirmed asthenozoospermia were enrolled. Whole-exome sequencing (WES) was performed on genomic DNA from peripheral blood, and the candidate variant was validated by Sanger sequencing. Functional predictions were made using PolyPhen-2, SIFT, MutationTaster, and REVEL. TACR3 mRNA expression levels were assessed by real-time PCR in available samples. RESULTS: A novel splice-site variant, TACR3 (NM_001059.3:c.888 + 1G > A), was detected and found to segregate with infertility in one family, appearing homozygously in two infertile brothers and heterozygously in the proband with severe asthenozoospermia. The variant was absent in public and local genomic databases, suggesting its extremely rare frequency. Furthermore, RT-PCR showed a dramatic reduction or complete loss of TACR3 expression in affected individuals, confirming its deleterious effect on splicing and mRNA stability. CONCLUSION: We identified a previously unreported splice-site mutation in TACR3 (c.888 + 1G > A) that likely causes familial infertility by disrupting the neurokinin B/NK3R signaling pathway. While the heterozygous proband exhibited severe asthenozoospermia, the homozygous brothers displayed hormonal profiles typical of hypogonadotropic hypogonadism. These findings extend the mutational landscape of TACR3 and highlight its essential contribution to male reproductive endocrinology.

Humans↗
PubMed1992

A Danish kindred with familial amyloid cardiomyopathy revisited: identification of a mutant transthyretin-methionine111 variant in serum from patients and carriers.

PURPOSE: In familial amyloid cardiomyopathy of Danish origin, the amyloid microfibrils contain a mutant transthyretin (TTR) with a methionine-for-leucine substitution at the molecular position 111. We studied the possible occurrence of this variant TTR-Met111 in serum from afflicted as well as nonafflicted family members and their offspring, in order to define its possible role as predictor of the disease and to describe its mode of inheritance. PATIENTS AND METHODS: Stored, frozen serum samples obtained from 1959 through 1960 from 36 of 40 living members of the kindred were analyzed. The method employed to detect the abnormal TTR was based on the electrophoretic separation of fragments produced by cyanogen bromide cleavage at the two methionine sites. RESULTS: All sera from family members with amyloid cardiomyopathy contained the variant transthyretin TTR-Met111 as did sera from half of their offspring. In contrast, nonafflicted family members and their offspring were seronegative for TTR-Met111. Three cousins from the second generation died between 1980 and 1986 of amyloid cardiomyopathy. The presence of variant TTR-Met111 preceded their deaths by 20 to 26 years. CONCLUSIONS: The occurrence in serum of the mutant transthyretin TTR-Met111 is linked to the occurrence of amyloid cardiomyopathy in patients and their offspring, while unafflicted branches of the family are negative for the variant protein. That the occurrence in serum of TTR-Met111 precedes the onset of clinical amyloid cardiomyopathy by several decades makes the variant TTR a marker for the disease. The distribution of afflicted family members and seropositivity for the variant TTR shows an autosomal dominant mode of inheritance. CLINICAL SIGNIFICANCE: The results make possible early detection of potential patients and provide tools for genetic counseling. Cardiac transplantation may provide a new therapeutic option.

Adult↗
PubMed1987

Identification and characterization of a human transthyretin variant.

An apparent Mr variant of plasma transthyretin (TTR), previously detected using 2-D PAGE, is the first reported occurrence of this type of human TTR variant. We characterized the variant TTR to determine the nature of this difference. Comparative tryptic peptide maps of variant and normal TTR and sequencing of peptides which differed indicated the variant contained a single amino acid substitution of valine for tyrosine at position 116. Because such a change requires two nucleotide substitutions, we postulate the variant arose through mutation in codon 116 of a heretofore unrecognized polymorphic or rare variant allele of TTR.

Amino Acid Sequence↗
PubMed1994

Expression of rat alpha-fetoprotein cDNA and its mutants in cultured mouse fibroblasts and identification of glycosylation sites related to electrophoretic variants.

Rat alpha-fetoprotein (RAFP) shows two discrete electrophoretic variants, slow and fast, with molecular weights of 72,500 and 69,500, respectively. To elucidate the structural basis of this heterogeneity, we developed the expression system of RAFP cDNA and its mutants with the use of cultured mouse fibroblasts and a retrovirus vector. This produced recombinant wild-type and three mutant proteins and has several advantages over the use of Escherichia coli or Saccharomyces cerevisiae. The mutants were designed to lack either one or both of the two possible glycosylation sites on RAFP. Electrophoretic analyses relating to the glycosylation states of the recombinant proteins as well as of natural RAFP produced by rat cells before and after digestion with glycopeptidase F indicated that the slow variant has carbohydrate units located at Asn-93 and Asn-229 and the fast one has one at Asn-229.

Amidohydrolases↗
PubMed1995

Identification and tissue distribution of a novel variant of 11 beta-hydroxysteroid dehydrogenase 1 transcript.

A novel variant of 11 beta-hydroxysteroid dehydrogenase 1 (11 beta-HSD1) mRNA was identified from the ovine liver by reverse transcription-polymerase chain reaction (RT/PCR), and was named 11 beta-HSD1C mRNA. Sequence analysis of the RT-PCR product revealed that 11 beta-HSD1C mRNA was the product of an alternative exon-splicing within the 11 beta-HSD1 gene in which exon 5 was spliced out. Although it caused a deletion of 48 amino acids in the deduced 11 beta-HSD1 protein, this alternative splicing did not result in a shift within the predicted open reading frame of 11 beta-HSD1 cDNA. Thus, 11 beta-HSD1C mRNA was predicted to code for a protein of 244 amino acids. Using RT-PCR, we also examined the expression of 11 beta-HSD1C mRNA in ovine fetal organs and in maternal myometrium, endometrium, chorion, amnion and placenta. The 11 beta-HSD1C mRNA was expressed ubiquitously, similar to 11 beta-HSD1A mRNA, but at a lower abundance. Furthermore, since levels of 11 beta-HSD1C mRNA were directly related to those of 11 beta-HSD1A mRNA, there is no tissue-specificity for this shorter transcript and the only factor regulating its production appears to be 11 beta-HSD1A mRNA itself. To determine whether 11 beta-HSD1C mRNA encoded a functional enzyme, we inserted the cDNA into the expression vector pRc/CMV, and transfected the construct into Chinese hamster ovary cells. The transfected cells expressed a mRNA of expected size but contained no detectable 11 beta-HSD activity. When combined with cellular extracts of 11 beta-HSD1A cDNA transfected cells, they also did not alter either the dehydrogenase or reductase activity. The functional significance of the 11 beta-HSD1 transcript lacking exon 5 (11 beta-HSD1C mRNA) remains to be determined.

11-beta-Hydroxysteroid Dehydrogenases↗
PubMed2005

Identification and characterization of a novel splice variant of beta3 subunit of GABA(A) receptor in rat testis and spermatozoa.

Gamma-aminobutyric acid type A (GABA(A)) receptors are the major sites of inhibitory action of fast synaptic neurotransmission in the brain. Their receptors are also widely distributed in peripheral and endocrine tissues. A full-length cDNA encoding a novel splice variant of beta3 subunit of GABA(A) receptor, designated as beta3t, was identified in rat testis. This isoform contains a segment, having identical amino acid sequence as the beta3 subunit of neuronal GABA(A) receptors except for a section composed of 25 different amino acid sequence in the N-terminus. Northern blot shows that this isoform is found in rat testis. The beta3t isoform mRNA was detected in germ cells in the late step of spermatogenesis by in situ hybridization assay. Results of immunohistochemical and immunocytochemical assays indicate that the beta3t isoform is expressed in rat testis and spermatozoa. To determine a possible function of the N-terminal 25 amino acid segment, a recombinant plasmid of beta3t-EGFPC was constructed by fusing green fluorescent protein to the C-terminus of the beta3t isoform. The chimera product failed to be translocated unto the cell surface when expressed in HEK 293 cells; whereas, the beta3 subunit of rat brain is incorporated into the plasma membrane. In conclusion, the present results show that one variant of beta3 subunit of GABA(A) receptor, designated as beta3t, is found in germ cells of rat testis and sperm. The inability of the beta3t variant to target into the plasma membrane maybe a consequence of the unique 25 amino acid segment in the N-terminus.

Alternative Splicing↗
PubMed2005

Identification and characterisation of a novel splice variant of the human CB1 receptor.

Cannabinoid ligands are implicated in many physiological processes and to date two receptors have been identified. However, a growing body of evidence exists that suggests the presence of additional receptors. Whilst cloning the previously described hCB1a, we have identified a novel variant that we call hCB1b. Characterising these two splice variants demonstrates that they have a unique pharmacological profile and that their RNA's are expressed at low levels in a variety of tissues.

Alternative Splicing↗
PubMed2006

Identification and expression analysis of alternative splice variants of the rat Hax-1 gene.

Hax-1 protein, which has been studied in mice and humans, shows a potent anti-apoptotic activity and is involved in regulation of cell motility. Cloning of the rat Hax-1 cDNA has revealed seven alternative transcripts, which differ mostly in their 5' region. Alternative splicing concerns exon 1, skipped in 5 transcripts, intron 1 which is partially retained in these transcripts, exon 2, which can be partially skipped, and intron 2, retained in one variant. The existence of different splicing variants was confirmed by exon-junction-specific RT-PCR and RNase protection assay. Analysis of expression indicates that overall Hax-1 mRNA level is relatively low in most tissues and very high in testes, and that the expression pattern of the variants is similar in different tissues. Presence of different transcripts implies the existence of several protein isoforms, with three putative start codons. The existence of at least three protein isoforms was confirmed by Western blot. Interestingly, high mRNA level in testes does not translate into high protein level, suggesting the existence of tissue-specific translational regulation or regulated protein degradation.

Alternative Splicing↗
PubMed2026

Identification of Two Novel Compound Heterozygous ADAMTS17 Variants Associated With Weill-Marchesani Syndrome 4.

PURPOSE: Weill-Marchesani syndrome 4 (WMS4) is frequently underdiagnosed when standard exome sequencing fails to detect noncoding pathogenic variants. We aimed to identify the genetic cause in a patient with suspected WMS4 and to characterize the splicing-altering mechanism of a deep intronic variant in ADAMTS17. MATERIALS AND METHODS: Whole-exome sequencing combined with whole-genome sequencing was conducted in the proband, who presented with ocular and skeletal manifestations of WMS4. A minigene splicing assay was applied to verify the splicing abnormality caused by the deep intronic variant. RESULTS: The patient showed high myopia, brachydactyly, accelerated growth velocity, and advanced bone age. Two novel compound heterozygous variants in ADAMTS17, c.1655G>A and c.450+38C>A, were identified. The deep intronic variant c.450+38C>A was confirmed by minigene assay to disrupt normal pre-messenger RNA splicing by inducing retention of a 35-base pair intronic segment, leading to a frameshift and premature termination (p.G152Lfs*23). CONCLUSIONS: This study broadens the mutational spectrum of ADAMTS17. Whole-genome sequencing combined with functional splicing validation is essential for resolving molecularly undiagnosed cases of WMS4, particularly when deep intronic variants are suspected, and supports clinical genetic testing and genetic counseling of hereditary connective tissue disorders.

ADAMTS17↗
PubMed2005

Identification and characterization of a novel Delphilin variant with an alternative N-terminus.

Delphilin is identified as a Glutamate receptor delta2 (GluRdelta2) subunit interacting protein, consisting of a PDZ domain and formin homology (FH) domains 1 and 2, in addition to a C-terminal coiled-coil structure. Delphilin has been shown to be selectively expressed in cerebellar Purkinje cells where it co-localizes with the GluRdelta2 subunit at the Purkinje cell-parallel fiber synapses. Although Delphilin specifically interacts with the GluRdelta2 C-terminus via its PDZ domain, the physiological role of the interaction is not yet understood. Here, we report that the Delphilin protein exhibits diversity at its N-terminus by variable usage of the first several exons. Interestingly, the two Delphilin mRNAs which correspond to the first one initially identified (now designated as Delphilin alpha) and the second that contains a newly identified first exon (designated as Delphilin beta), show different chronological expression profiles. Delphilin beta mRNA was not decreased throughout the cerebellar development in vivo and in vitro, while in vivo Delphilin alpha mRNA gradually decreases following the first postnatal week. Delphilins alpha and beta also revealed different subcellular distribution with some overlap. Specifically, the cerebellar synaptosomal membrane fraction contained the Delphilin beta protein. Both Delphilin alpha and beta localized at the dendritic spines with GluRdelta2; however, dendritic shafts in cultured Purkinje cells also included Delphilin beta. In MDCK cells upon becoming confluent, Delphilin alpha moved to the cell-cell junction area, whereas Delphilin beta maintained a diffuse distribution pattern throughout the cytoplasm. Taken as a whole, these two different Delphilins seemed to play functionally different roles in developing and matured cerebellar Purkinje cells.

Alternative Splicing↗
PubMed2004

PXR (NR1I2): splice variants in human tissues, including brain, and identification of neurosteroids and nicotine as PXR activators.

To gain insight on the expression of pregnane X receptor (PXR), we analyzed PXR.1 and PXR alternatively spliced transcripts in a panel of 36 human tissues. PXR.1 was expressed in many more tissues than previously determined, including human bone marrow and select regions of the human brain. In each of these tissues, we observed alternative splicing of various exons of PXR that generated multiple distinct PXR isoforms. The most abundant PXR alternative mRNA transcripts lacked 111 nucleotides, deleting 37 amino acids from the PXR LBD (PXR.2), or lacked 123 nt, deleting 41 amino acids from the PXR LBD (PXR.3). CYP3A4, a gene transcriptionally regulated by PXR, showed incomplete overlap with PXR in its tissue distribution. Quantitation of PXR mRNAs in human liver demonstrated that PXR.2 and PXR.3 represented 6.7% and 0.32% of total PXR mRNA transcripts. Brain expression of PXR prompted analysis of whether some brain acting chemicals were PXR ligands. The neurosteroids allopregnanolone and pregnanolone activated PXR and induced transcription of a CYP3A4-luciferase reporter. Nicotine, the psychoactive and addictive chemical in cigarettes, and a known inducer of brain CYP2B6, was an efficacious activator of PXR and inducer of CYP3A4 transcription. Because nicotine activation of PXR will enhance metabolism of nicotine to the non-psychoactive cotinine, these results provide one molecular mechanism for the development of tolerance to nicotine. Moreover, the identification of PXR in many human tissues, such as brain, and activation by tissue specific ligands (such as neurosteroids) suggests additional biological roles for this receptor in these tissues.

Adult↗
PubMed1997

Identification and tissue expression of a splice variant for the growth arrest-specific gene gas6.

The growth arrest-specific gene gas6 encodes a secreted protein (Gas6) which is a member of the vitamin K-dependent protein family and was identified as a ligand for the Ax1 tyrosine kinase receptor family. Gas6 shares significant similarity with protein S and a similar domain organisation: an extensively gamma-carboxylated amino-terminal, four epidermal growth factor-like motifs and a large carboxy-terminal region, known as the D domain. Here we report on the isolation of a splice variant (gas6SV) characterised by an in-frame 129 bp insertion between the fourth EGF domain and the D domain. The gene gas6 was previously mapped on chromosome 13. The genomic organisation of gas6 has been investigated demonstrating the presence of alternative splicing consensus sites. Expression of gas6SV has been investigated in various human tissues and found to have a similar distribution pattern as gas6, with the exception of the spleen where gas6SV seems to be the predominant form.

Alternative Splicing↗