Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “coding variants”

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 1,657 records · Page 92Linked to original sources
PubMed1980

Messenger RNA coding for the deleted heavy chain of mouse myeloma MOPC 47A immunoglobulin.

Mouse IgA 47A is an immunoglobulin variant whose heavy (alpha) chain has a molecular weight of 40,000 and lacks the entire CH3 domain. In order to understand better the mechanism by which the CH3 domain is lost, the 47A heavy chain mRNA has been partially purified. The mRNA migrated as a 17 S species on sucrose gradients and coded for the cell-free synthesis of only one serologically reactive protein with an apparent molecular weight of 42,000. Competitive inhibition of immunoprecipitation and tryptic peptide analysis of a cyanogen bromide fragment of the in vitro product revealed significant homology between the authentically secreted heavy chain and the respective cell-free synthesized, immunoprecipitated product. The heavy chain mRNA of 47A possessed a chain length of about 2200 nucleotides which is the same size as a normal alpha heavy chain mRNA, thus demonstrating that the protein deletion is not due to a large deletion at the mRNA level. The deletion in the 47A heavy chain may be due to a frameshift of a single nucleotide followed by premature chain termination.

Animals↗
PubMed2007

Sequence variants within exon 1 of MECP2 occur in females with mental retardation.

A new splice variant of the Rett syndrome gene, MECP2, was recently identified, that includes coding sequence from exon 1, and is the predominant transcript in the central nervous system. This sequence encodes polyalanine and polyglycine stretches within the N-terminal portion of MeCP2, and may confer novel functional properties to the protein. We screened autism, mental retardation (MR), and control populations for sequence variation within this region, and identified variation in approximately 1% of MR cases screened (N = 1,410). No variants were identified in the autism sample (N = 401). Most of these variants occur within a trinucleotide repeat region and result in change in number of alanine or glycine residues within the repeat stretches. We suggest some of these variants may be a relatively frequent cause of non-specific MR or developmental delay.

Adult↗
PubMed2004

Functional analysis of MOR-1 splice variants of the mouse mu opioid receptor gene Oprm.

A series of mu opioid receptor gene Oprm splice variants have been reported that differ only at their C-terminus. These variants all contain exons 1, 2, and 3 of the gene, the exons responsible for coding all seven transmembrane domains. Whereas MOR-1 also has exon 4 that encodes for an additional 12 amino acids at the tip of the C-terminus, the other MOR-1 variants have unique amino acid sequences distinct from those in MOR-1 due to alternative splicing. All these variants are mu-selective in binding assays. The current study explored the ability of these variants to stimulate [35S]GTPgammaS binding to assess them functionally. Only mu opioids stimulated [35S]GTPgammaS binding. Among the mu opioids we noted marked differences in their maximal stimulation among the clones. This was most prominent with beta-endorphin, which stimulated [35S]GTPgammaS binding in the MOR-1E expressing cells to a greater degree than [D-Ala2,MePhe4,Gly(ol)5]enkephalin (DAMGO; 130%) and was far less effective than DAMGO in MOR-1C cells (44%). The rank order of maximal stimulation of the drugs varied among the clones as well. Dynorphin A, beta-endorphin and morphine were most effective in stimulating [35S]GTPgammaS binding in MOR-1E, while M6G and fentanyl were most effective in MOR-1 expressing cells. The potency (EC50) of some of the drugs also varied extensively among the clones, with a poor correlation between the potency of the drugs to stimulate [35S]GTPgammaS binding and their binding affinity. Together, these findings reveal marked functional differences among the variants that only can be explained by their structural differences at the tip of their C-terminus.

Alternative Splicing↗
PubMed2004

Little cherry virus-2: sequence and genomic organization of an unusual member of the Closteroviridae.

The complete genomic sequence of variant USA6b of Little cherry virus-2 (LChV-2), has been determined and is 15045 nucleotides in length, coding for 11 open reading frames (ORFs). The sequence shares 77.2% identity with a previously published, ca. 6 kb partial replicase sequence of LChV-2 (variant USA6a). Both LChV-2/USA6a and LChV-2/USA6b were obtained from the same tree infected with little cherry disease, and would suggest a mixed infection. LChV-2/USA6b is more closely related to the partially determined genomic sequence of a Canadian isolate of LChV-2, strain LC5 (92.9% identity). LChV-2/USA6b has an unusual genomic organization compared to other members of the Closteroviridae. The LChV-2/USA6b genome is potentially ambi-sense, with a negative sense ORF0 at the 5' terminus, from which an 18.1 kDa protein of unknown function can be expressed in vitro. The N-terminal region of the LChV-2/USA6 ORF1a translation product does not code for a papain-like protease motif. ORF1 codes for a novel motif, of unknown function, also present in isolates of the Grapevine leafroll associated virus-3, (genus Ampelovirus) as well as viruses of the family Flexiviridae. ORF3 lacks an AUG start codon, but could potentially be expressed via read-through of the ORF2 stop codon. At the 3' end, there is a re-organization of encoded genes compared with other members of the Closteroviridae including separation of the coat protein and coat protein duplicate genes by 4 other genes as found for LChV-2/LC5.

Amino Acid Sequence↗
PubMed2000

Novel transcripts of the estrogen receptor alpha gene in channel catfish.

Complementary DNA libraries from liver and ovary of an immature female channel catfish were screened with a homologous ERalpha cDNA probe. The hepatic library yielded two new channel catfish ER cDNAs that encode N-terminal ERalpha variants of different sizes. Relative to the catfish ERalpha (medium size; 581 residues) previously reported, these new cDNAs encode Long-ERalpha (36 residues longer) and Short-ERalpha (389 residues shorter). The 5'-end of Long-ERalpha cDNA is identical to that of Medium-ERalpha but has an additional 503-bp segment with an upstream, in-frame translation-start codon. Recombinant Long-ERalpha binds estrogen with high affinity (K(d) = 3. 4 nM), similar to that previously reported for Medium-ERalpha but lower than reported for catfish ERbeta. Short-ERalpha cDNA encodes a protein that lacks most of the receptor protein and does not bind estrogen. Northern hybridization confirmed the existence of multiple hepatic ERalpha RNAs that include the size range of the ERalpha cDNAs obtained from the libraries as well as additional sizes. Using primers for RT-PCR that target locations internal to the protein-coding sequence, we also established the presence of several ERalpha cDNA variants with in-frame insertions in the ligand-binding and DNA-binding domains and in-frame or out-of-frame deletions in the ligand-binding domain. These internal variants showed patterns of expression that differed between the ovary and liver. Further, the ovarian library yielded a full-length, ERalpha antisense cDNA containing a poly(A) signal and tail. A limited survey of histological preparations from juvenile catfish by in situ hybridization using directionally synthesized cRNA probes also suggested the expression of ERalpha antisense RNA in a tissue-specific manner. In conclusion, channel catfish seemingly have three broad classes of ERalpha mRNA variants: those encoding N-terminal truncated variants, those encoding internal variants (including C-terminal truncated variants), and antisense mRNA. The sense variants may encode functional ERalpha or related proteins that modulate ERalpha or ERbeta activity. The existence of ER antisense mRNA is reported in this study for the first time. Its role may be to participate in the regulation of ER gene expression.

3' Untranslated Regions↗
PubMed2005

Worldwide haplotype diversity and coding sequence variation at human bitter taste receptor loci.

Bitter taste perception in humans is mediated by receptors encoded by 25 genes that together comprise the TAS2R (or T2R) gene family. The ability to identify the ligand(s) for each of these receptors is dependent on understanding allelic variation in TAS2R genes, which may have a significant effect on ligand recognition. To investigate the extent of coding variation among TAS2R alleles, we performed a comprehensive evaluation of sequence and haplotype variation in the human bitter taste receptor gene repertoire. We found that these genes exhibit substantial coding sequence diversity. In a worldwide population sample of 55 individuals, we found an average of 4.2 variant amino acid positions per gene. In aggregate, the 24 genes analyzed here, along with the phenylthiocarbamide (PTC) receptor gene analyzed previously, specify 151 different protein coding haplotypes. Analyses of the ratio of synonymous and nonsynonymous nucleotide substitutions using the Ka/Ks ratio revealed an excess of amino acid substitutions relative to most other genes examined to date (Ka/Ks = 0.94). In addition, comparisons with more than 1,500 other genes revealed that levels of diversity in the TAS2R genes were significantly greater than expected (pi = 0.11%; p < 0.01), as were levels of differentiation among continental populations (FST = 0.22; p < 0.05). These diversity patterns indicate that unusually high levels of allelic variation are found within TAS2R loci and that human populations differ appreciably with respect to TAS2R allele frequencies. Diversity in the TAS2R genes may be accounted for by natural selection, which may have favored alleles responsive to toxic, bitter compounds found in plants. These findings are consistent with the view that different alleles of the TAS2R genes encode receptors that recognize different ligands, and suggest that the haplotypes we have identified will be important in studies of receptor-ligand recognition.

Alleles↗
PubMed1999

Integrin subunits (beta)1C-1 and (beta)1C-2 expressed in GD25T cells are retained and degraded intracellularly rather than localised to the cell surface.

We have previously identified the integrin (beta)1C-2 and characterised the distribution of (beta)1C-1 and (beta)1C-2 transcripts in various cell lines and normal cells. In this study we have investigated the expression of the two (beta)1C-variants in integrin (beta)1 deficient mouse GD25T cells. After stable transfection of the GD25T cells with cDNAs coding for (beta)1A, (beta)1C-1 and (beta)1C-2, the cell surface expression of the (beta)1C-1 and (beta)1C-2 variants was found to be very low while the (beta)1A variant was expressed at high levels. Northern blot analysis showed that the level of (beta)1-transcript in the (beta)1C-1 and (beta)1C-2 clones was equal or higher than in the (beta)1A clones. Metabolic labelling and deglycosylation by endoglycosidase H treatment clearly demonstrated that the majority of the (beta)1C-1 and (beta)1C-2 chains did not become maturely glycosylated, nor did they dimerize with (alpha) subunits. After 20 hours of chase, the labelled (beta)1C-1 and (beta)1C-2 chains had been gradually degraded, whereas immature (beta)1A was converted into the maturely glycosylated form during the same period of time. Immunostaining showed intracellular (beta)1 localisation in the (beta)1C-1 and (beta)1C-2 expressing clones, while in the (beta)1A expressing clones the (beta)1 chains were mainly localised to focal adhesion sites and along fibronectin fibres. Taken together, we have shown that expression of both integrin (beta)1C-1 and (beta)1C-2 in GD25T cells result in very low cell surface expression compared with the normal (beta)1A isoform. Instead, both (beta)1C-1 and (beta)1C-2 chains remain in the endoplasmic reticulum until they are intracellularly degraded.

Animals↗
PubMed1997

Analysis of islet regenerating (reg) gene polymorphisms in fibrocalculous pancreatic diabetes.

Fibrocalculous pancreatic diabetes (FCPD) is a form of diabetes associated with tropical chronic calcific pancreatitis, seen mostly in developing countries. FCPD is likely to be a multifactorial disease with both environmental and genetic components. The reg 1A gene encodes a protein associated with regeneration of pancreatic islets and has a sequence identical to that of pancreatic stone protein. Since FCPD is associated with both diabetes and pancreatitis, we tested the hypothesis that FCPD may be the result of mutations in the coding regions of the reg 1A gene. Restriction length polymorphisms (RFLPs) and possible sequence variants of the reg 1A gene were studied by RFLP analysis, looking for single-stranded conformational polymorphisms (SSCPs) and direct nucleotide sequencing. In 20 patients with FCPD and 20 control subjects, no RFLPs were detected using 10 restriction enzymes. In 50 patients with FCPD and 50 control subjects, no SSCP variants were detected. Finally, direct nucleotide sequencing of the reg 1A gene from 30 patients with FCPD did not show any differences from the published human reg 1A gene sequence. In conclusion, it seems unlikely that mutations in the coding region of the reg 1A gene are a common cause of FCPD.

Calcinosis↗
PubMed2004

Human poly(ADP-ribose) glycohydrolase is expressed in alternative splice variants yielding isoforms that localize to different cell compartments.

Poly(ADP-ribose) glycohydrolase (PARG) is the only protein known to catalyze hydrolysis of ADP-ribose (ADPR) polymers to free ADP-ribose. While numerous genes encode different poly(ADP-ribose) polymerases (PARPs) that all synthesize ADP-ribose polymer, only a single gene coding for PARG has been detected in mammalian cells. Here, we describe two splice variants of human PARG mRNA, which lead to expression of PARG isoforms of 102 kDa (hPARG102) and 99 kDa (hPARG99) in addition to the full-length PARG protein (hPARG111). These splice variants differ from hPARG111 by the lack of exon 1 (hPARG102) or exons 1 and 2 (hPARG99). They are generated by the utilization of ambiguous splice donor sites in the PARG gene 5' untranslated region. The hPARG111 isoform localizes to the nucleus, whereas hPARG102 and hPARG99 are cytoplasmic proteins. The nuclear targeting of hPARG111 is due to a nuclear localization signal (NLS) in exon 1 that was mapped to the amino acids (aa) (10)CTKRPRW(16). Immunocytochemistry, immunoblotting, and PARG enzyme activity measurements show that the cytoplasmic isoforms of PARG account for most of the PARG activity in cells in the absence and presence of genotoxic stress. The predominantly cytoplasmic location of cellular PARG is intriguing as most known cellular PARPs have a nuclear localization.

5' Untranslated Regions↗
PubMed1995

Structure and regulation of the luteinizing hormone receptor gene.

Studies of the mechanisms controlling the expression of the rat luteinizing hormone receptor gene were pursued by characterization of the gene structure and identification of regulatory protein binding domains in the 5'-non-coding region of the gene and of 3' non-coding functional domains responsible for generation of the major mRNA forms. The coding region of the rat LHR gene contains 10 introns and 11 exons, of which the first 10 exons comprise the hormone binding extracellular domain and exon 11, the seven transmembrane/G protein coupling module. Several alternative spliced variants of the LHR were identified that conform to deletions of complete and/or partial exons. Within the 6.2 kb of the 3'-non-coding region, two functional LHR pA domains (H1) and (H2) produce two sets of major mRNA transcripts, each coding for both holoreceptor and the form B splice variant. The H1 pA domain is unique to LHR and may represent a recombinant insertion domain. The functional efficiency of each pA domain is related to the specific pA signals, distal downstream elements, and tissue-specific factors. A TATA-less promoter region is present within the 173 bp 5'flanking region of the gene, with Initiator (Inr) elements at transcriptional start sites. Transcription is dependent on the binding of the Sp1 protein at two Sp1 domains that each contribute equally to transcript initiation. Promoter activity is regulated by at least three additional DNA domains, R (-1266 to -1307 bp), C-box (-42 to -73 bp) and M1 (-24 to -42 bp) that bind multiple trans-factors in a tissue-specific manner. Basal promoter activity is enhanced by a functional M1 domain in LHR-expressing mouse Leydig tumor cells (MLTC) but not in non-expressing CHO cells. C-box binding factors either inhibit promoter activity or block inhibition through overlapping but not identical DNA binding domains that carry AP-2 and NF-1 elements. Removal of the AP-2 element within the C-box results in MLTC-specific transcriptional activation that may involve an MTLC M1/C-box interaction. In addition, competition for C-box factors by an upstream regulatory element (R) that is only inhibitory in CHO cells, indicates that both C-box binding factors compete for this upstream (R) domain in a tissue-specific manner. Competition between the inhibitory and neutral DNA binding factors within both upstream (R) and promoter domains (C-box) could provide a mechanism for the control of LH receptor gene expression in gonadal cells.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2004

Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms.

MOTIVATION: Single nucleotide polymorphisms (SNPs) are the most common form of genetic variant in humans. SNPs causing amino acid substitutions are of particular interest as candidates for loci affecting susceptibility to complex diseases, such as diabetes and hypertension. To efficiently screen SNPs for disease association, it is important to distinguish neutral variants from deleterious ones. RESULTS: We describe the use of Pfam protein motif models and the HMMER program to predict whether amino acid changes in conserved domains are likely to affect protein function. We find that the magnitude of the change in the HMMER E-value caused by an amino acid substitution is a good predictor of whether it is deleterious. We provide internet-accessible display tools for a genomewide collection of SNPs, including 7391 distinct non-synonymous coding region SNPs in 2683 genes. AVAILABILITY: http://lpgws.nci.nih.gov/cgi-bin/GeneViewer.cgi

Amino Acid Motifs↗
PubMed1993

Expression of the D3 dopamine receptor gene and a novel variant transcript generated by alternative splicing in human peripheral blood lymphocytes.

The sequential reverse transcription and polymerase chain reaction amplified the mRNA coding for the D3 dopamine receptor (D3R) in human peripheral blood lymphocytes. Pharmacological analysis confirmed the binding of the D3R specific ligand to the lymphocytes. In addition, there was a novel shorter variant transcript of the D3R gene generated by alternative splicing in lymphocytes and brain. This variant, termed D3(TM4-del), has a 143 bp deletion and encodes a 138 amino acid protein containing the first three transmembrane domains of the native D3R.

Adult↗
PubMed1998

Novel variant of the P2X2 ATP receptor from the guinea pig organ of Corti.

ATP functions as a neurotransmitter and a neuromodulator in various tissues by acting on metabotropic (P2Y) and ionotropic (P2X) receptors. Evidence suggests that ATP activates P2X receptors on several cell types in the organ of Corti of guinea pig including outer hair cells (OHCs), Deiters' cells, Hensen's cells, pillar cells and inner hair cells (IHCs). Determining the sequence and structure of P2X receptors in guinea pig organ of Corti is important for understanding the function of ATP in the cochlea. We screened a guinea pig organ of Corti cDNA library for P2X2 ATP receptors using rat P2X2 cDNA as a probe. We sequenced three P2X2 variants which were found to be abundant in this library. One is a novel P2X2 isoform (P2X2-3) created by a retained intron coding for an additional 27 amino acids (81 bp) in the putative extracellular domain. We have also sequenced a variant (P2X2-2) that lacks both the 81-bp sequence and a 192-bp sequence in the 3' intracellular domain. A third variant (P2X2-1) contains the intracellular 192-bp sequence but not the extracellular 81-bp sequence found in P2X2-3. The multiple transcripts arise from alternative intron and exon splicing events. In situ hybridization with a probe common to the three variants localized P2X2 to many of the cells of the organ of Corti.

Adenosine Triphosphate↗
PubMed1983

Deletion and amplification of DNA sequences in melanin-negative variants of Streptomyces reticuli.

The sporulating wild type of Streptomyces reticuli produces the pigment melanin. Though the ability to synthesize tyrosinase is frequently lost, it was demonstrated, that the structural gene coding for this enzyme is not located on the extrachromosomal DNA of the wild type strain or melanin-positive variants. Melanin negative variants were found to have lost this gene and to contain amplified nucleotide sequences within their genomes.

Catechol Oxidase↗
PubMed2005

Identification of FOXP2 truncation as a novel cause of developmental speech and language deficits.

FOXP2, the first gene to have been implicated in a developmental communication disorder, offers a unique entry point into neuromolecular mechanisms influencing human speech and language acquisition. In multiple members of the well-studied KE family, a heterozygous missense mutation in FOXP2 causes problems in sequencing muscle movements required for articulating speech (developmental verbal dyspraxia), accompanied by wider deficits in linguistic and grammatical processing. Chromosomal rearrangements involving this locus have also been identified. Analyses of FOXP2 coding sequence in typical forms of specific language impairment (SLI), autism, and dyslexia have not uncovered any etiological variants. However, no previous study has performed mutation screening of children with a primary diagnosis of verbal dyspraxia, the most overt feature of the disorder in affected members of the KE family. Here, we report investigations of the entire coding region of FOXP2, including alternatively spliced exons, in 49 probands affected with verbal dyspraxia. We detected variants that alter FOXP2 protein sequence in three probands. One such variant is a heterozygous nonsense mutation that yields a dramatically truncated protein product and cosegregates with speech and language difficulties in the proband, his affected sibling, and their mother. Our discovery of the first nonsense mutation in FOXP2 now opens the door for detailed investigations of neurodevelopment in people carrying different etiological variants of the gene. This endeavor will be crucial for gaining insight into the role of FOXP2 in human cognition.

Alternative Splicing↗
PubMed2003

Biophysical analyses of the transthyretin variants, Tyr114His and Tyr116Ser, associated with familial amyloidotic polyneuropathy.

The familial amyloidotic polyneuropathy is strictly associated with point mutations in the coding region of the transthyretin gene. Here, we focused on the mutations in the monomer-monomer and dimer-dimer interaction site of the transthyretin tetramer. The naturally occurring amyloidogenic Tyr114His (Y114H) and Tyr116Ser (Y116S) variants formed more amyloid fibrils than the wild-type transthyretin, nonamyloidogenic Tyr116Val (Y116V) variant, and other amyloidogenic variants in previous studies. The secondary, tertiary, and quaternary structural stabilities of the Y114H and Y116S variants were compared with those of the wild-type transthyretin and nonamyloidogenic Y116V variant. The unfolding data indicated that the amyloidogenic Y114H and Y116S mutations reduced the stability of the secondary, tertiary, and quaternary structure. Our results also indicated that the unfolding of Y114H and Y116S is less cooperative than that of the wild-type transthyretin. Moreover, the tetramer of the amyloidogenic variants dissociated to the monomer even at pH 7.0, indicating the importance of Tyr114 and Tyr116 in strengthening the contacts between monomers and/or dimers of the transthyretin molecule.

Amino Acid Substitution↗
PubMed1987

Alpha 1-antitrypsin deficiency--a defect in secretion.

A naturally occurring point mutation in the human alpha 1-antitrypsin gene leads to the synthesis of a variant of the protein which is poorly secreted from hepatocytes. This Z mutation codes for a glutamic acid to lysine substitution at residue 342 in the polypeptide chain. The mutant protein is correctly translocated into the lumen of the endoplasmic reticulum and core glycosylated but inefficiently transported beyond the ER compartment. Experiments using Xenopus oocytes as a surrogate secretory cell show that abberant secretion of the variant is not confined to hepatocytes and glycosylation of the polypeptide is not obligatory for the block in secretion. Site-directed mutagenesis can be used to examine the effect of natural mutations on protein structure and the relationship between structure and intracellular transport.

Animals↗
PubMed2007

Cloning, expression, and characterization of an alternatively spliced variant of human heparanase.

Heparanase is an endoglycosidase that cleaves heparan sulfate in the extracellular matrix (ECM) and hence participates in ECM degradation and remodeling. Heparanase is involved in fundamental biological processes such as cancer metastasis, angiogenesis, and inflammation. Alternative splicing in the coding region of human heparanase was not reported. Here, we report the cloning of a splice variant of human heparanase that lacks exon 5 and is missing 174 bp compared to the wild-type cDNA. Splice 5 is expressed as a 55 kDa protein compared to the 65 and 50 kDa latent and active wild-type enzyme. Splice 5 was not detected in the incubation medium of tumor cells as opposed to the wild-type latent heparanase. Splice 5 escaped proteolytic cleavage, was devoid of HS degradation activity and exhibited diffused rather than granular cellular localization.

Alternative Splicing↗