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Factor IX Zutphen. A genetic variant of blood coagulation factor IX with an abnormally high molecular weight.

A genetic variant of blood coagulation factor IX has been isolated from the plasma of a patient with severe hemophilia B (congenital factor IX deficiency). The isolated variant--factor IX Zutphen--has a strongly reduced affinity for binding of Ca2+, it cannot be cleaved proteolytically by factor XIa, and it has a molecular weight of about 90,000, which is much higher than the 65,000 found for normal factor IX and acarboxy factor IX. Available data indicate that these unique properties of factor IX Zutphen are connected with the presence of an extra polypeptide (molecular weight 33,000) that is linked to the factor IX molecule by a disulfide bond and thus prevents effective binding of Ca2+ or factor XIa. Such a model might explain the extremely low specific coagulant activity of factor IX Zutphen.

Blood Protein Electrophoresis↗

[Characterization of genetic variants of human albumin by isoelectric focusing].

Normal human serum albumin and bisalbuminic fractions from genetic variants of european origin have been studied by ultrathin-layer isoelectric focusing performed on whole sera or after purification of albumin fractions by affinity chromatography on Blue-Trisacryl. Narrow range ampholytes giving pH gradient between 5 and 8, together with the use of 8 M urea, provided suitable patterns allowing to discriminate the various allotypes. In these conditions, both normal albumin and heterozygous variants were microheterogeneous with several main bands; in the case of normal albumin, four major bands were found, while variants exhibited additional bands differing in number and pI. The position of additional bands comparatively to that of normal albumin was consistent with the electrophoretic behavior of variants. Fast moving allotypes exhibited additional bands with more anodal pIs, whereas slow moving variants were characterized by cathodal additional bands. The number and position of these bands allowed to characterize some variants, when they failed to distinguish between some others, identical patterns being correlated to identical mutations arising at different locations on the albumin molecule. These observations indicate that isoelectric focusing could allow a clear distinction of albumin variants, provided that their mutation were different, or could confirm the occurrence of identical mutation when IEF patterns are indistinguishable. In addition to electrophoretic mobilities at various pH, analytical isoelectric focusing could be a useful technique employed as a second step in the identification of allotypes prior to the determination of the structural change characterizing the variant.

Blotting, Western↗

Evaluation of genetic variants in the reduced folate carrier and in glutamate carboxypeptidase II for spina bifida risk.

Genetic variants in folate metabolism have been reported to increase risk for neural tube defects (NTD). The first such sequence change was the 677C-->T substitution in methylenetetrahydrofolate reductase (MTHFR), but additional sequence changes have been identified in enzymes or transporters for folates. Two recently identified variants are the 1561C-->T (H475Y) mutation in glutamate carboxypeptidase II (GCPII) and the 80A-->G (H27R) change in the reduced folate carrier RFC-1. We examined a group of mothers of spina bifida offspring, and a group of control women, for the above polymorphisms to assess their impact on NTD risk as well as on homocysteine and nutrient (RBC folate, serum folate, and serum cobalamin) levels. The GCPII variant (in the heterozygous state) did not influence NTD risk or metabolite levels; homozygous mutant (YY) women were not observed in our study group. The homozygous mutant (RR) genotype for the RFC-1 gene was not associated with a significant difference in NTD risk (OR=1.39, 95% CI=0.55-3.54), but there was a borderline significant (p=0.065) decrease in RBC folate levels, compared with the HH genotype. However, the combination of the RR genotype for RFC-1 and low RBC folate was associated with a significant 4.6-fold increase in NTD risk (OR=4.6, 95% CI=1.47-14.37). Since this small study is the first to demonstrate increased risk for women with the RFC-1 variant for having a child with a NTD, additional larger studies are required to confirm this change as another potential genetic modifier for spina bifida risk.

Alleles↗

Do hyporesponsive genetic variants of the melanocortin 1 receptor contribute to the etiology of multiple sclerosis?

Hyporesponsive genetic variants of the melanocortin 1 receptor result in pigmentary phenotypes exhibiting light skin and light color hair, including red hair. These variants are common in populations with high rates of multiple sclerosis, while rare in populations with low rates. Alpha-melanocyte stimulating hormone, the major ligand for this receptor, is responsible for phenotype determination, but is also known for its anti-inflammatory and immune modulating effects, including inhibition of factors implicated in multiple sclerosis pathology. As the melanocortin 1 receptor is expressed on various cell types involved in immune response, it is possible that carriers of hyporesponsive variants of this receptor lack the full anti-inflammatory and immune modulating effects of alpha-melanocyte stimulating hormone. It is proposed that these variants are part of a spectrum of genes involved in the etiology of multiple sclerosis. Related aspects of multiple sclerosis epidemiology are examined.

Clinical Trials as Topic↗

Implications of small effect sizes of individual genetic variants on the design and interpretation of genetic association studies of complex diseases.

Accumulated evidence from searching for candidate gene-disease associations of complex diseases can offer some insights as the field moves toward discovery-oriented approaches with massive genome-wide testing. Meta-analyses of 50 non-human lymphocyte antigen gene-disease associations with documented overall statistical significance (752 studies) show summary odds ratios with a median of 1.43 (interquartile range, 1.28-1.65). Many different biases may operate in this field, for both single studies and meta-analyses, and these biases could invalidate some of these seemingly "validated" associations. Studies with a sample size of >500 show a median odds ratio of only 1.15. The median sample size required to detect the observed summary effects in each population addressed in the 752 studies is estimated to be 3,535 (interquartile range, 1,936-9,119 for cases and controls combined). These estimates are steeply inflated in the presence of modest bias. Population heterogeneity, as well as gene-gene and gene-environment interactions, could steeply increase these estimates and may be difficult to address even by very large biobanks and observational cohorts. The one visible solution is for a large number of teams to join forces on the same research platforms. These collaborative studies ideally should be designed up front to also assess more complex gene-gene and gene-environment interactions.

Alleles↗

Polymorphism of complement component I in Mongoloid populations: a new genetic variant IF A2.

The genetic polymorphism of the complement component I (IF) was investigated in 282 Chinese, 239 Koreans and 198 Japanese. The 3 common IF phenotypes (A, AB and B) and a new rare IF phenotype (BA2) were observed. The obtained allele frequencies are as follows: IF*A = 0.0993 and IF*B = 0.9007 in Chinese; IF*A = 0.0921 and IF*B = 0.9079 in Koreans; IF*A = 0.0985, IF*B = 0.8990 and IF*A2 = 0.0025 in Japanese. These 3 Mongoloid populations showed a much higher degree of IF polymorphism than Caucasian populations.

Alleles↗

Genetic variants of human serum cholinesterase influence metabolism of the muscle relaxant succinylcholine.

People with genetic variants of cholinesterase respond abnormally to succinylcholine, experiencing substantial prolongation of muscle paralysis with apnea rather than the usual 2-6 min. The structure of usual cholinesterase has been determined including the complete amino acid and nucleotide sequence. This has allowed identification of altered amino acids and nucleotides. The variant most frequently found in patients who respond abnormally to succinylcholine is atypical cholinesterase, which occurs in homozygous form in 1 out of 3500 Caucasians. Atypical cholinesterase has a single substitution at nucleotide 209 which changes aspartic acid 70 to glycine. This suggests that Asp 70 is part of the anionic site, and that the absence of this negatively charged amino acid explains the reduced affinity of atypical cholinesterase for positively charged substrates and inhibitors. The clinical consequence of reduced affinity for succinylcholine is that none of the succinylcholine is hydrolyzed in blood and a large overdose reaches the nerve-muscle junction where it causes prolonged muscle paralysis. Silent cholinesterase has a frame shift mutation at glycine 117 which prematurely terminates protein synthesis and yields no active enzyme. The K variant, named in honor of W. Kalow, has threonine in place of alanine 539. The K variant is associated with 33% lower activity. All variants arise from a single locus as there is only one gene for human cholinesterase (EC 3.1.1.8). Comparison of amino acid sequences of esterases and proteases shows that cholinesterase belongs to a new family of serine esterases which is different from the serine proteases.

Amino Acid Sequence↗

Genetic variants of Tgfb1 act as context-dependent modifiers of mouse skin tumor susceptibility.

The human TGFB1 gene is polymorphic, and genetic variants are associated with altered cancer risk. However, human genetic association studies have had variable outcomes because TGFbeta1 action is context-dependent. We used the murine skin model of chemical carcinogenesis in genetic linkage analysis of three independent Mus musculus NIH/Ola x (Mus spretus x M. musculus NIH/Ola)F1 backcrosses, to identify a skin tumor susceptibility locus, Skts14, on proximal chromosome 7. Tgfb1 maps at the peak of linkage. The mouse Tgfb1 gene is polymorphic, resulting in cis-regulated differential allelic mRNA expression between M. spretus and M. musculus in F1 mouse skin. This phenomenon is reflected in differential phospho-SMAD2 levels, downstream of TGFbeta signaling, between these two mouse species. In normal F1 mouse skin, the Tgfb1SPR allele is expressed at higher levels than the Tgfb1NIH allele, and this differential is accentuated by phorbol 12-myristate 13-acetate treatment. In benign F1 papillomas, this imbalance is reversed, possibly by selection against expression of a hyperactive Tgfb1SPR allele in TGFbeta growth-responsive tumors. We demonstrate that skin tumor susceptibility is altered by Tgfb1 gene dosage, but that manifestation of Tgfb1-linked skin tumor susceptibility in M. musculus NIH/Ola x (M. spretus x M. musculus NIH/Ola)F1 backcross mice depends on interactions with another unlinked tumor modifying locus, Skts15, that overlaps Tgfbm3 on chromosome 12. These findings illustrate the power of complex genetic interactions in determining disease outcome and have major implications to the assessment of disease risk in individuals harboring variant TGFB1 alleles.

Alleles↗

Binding of disopyramide, methadone, dipyridamole, chlorpromazine, lignocaine and progesterone to the two main genetic variants of human alpha 1-acid glycoprotein: evidence for drug-binding differences between the variants and for the presence of two separate drug-binding sites on alpha 1-acid glycoprotein.

Human alpha 1-acid glycoprotein (AAG), a plasma drug transport protein, has three main genetic variants, the A variant and the F1 and S variants, which are encoded by two different genes. The binding of disopyramide, methadone, dipyridamole, chlorpromazine, lignocaine and progesterone to the two main gene products of AAG-the A variant and a mixture of the F1 and S variants (60% F1 and 40% S)-separated by chromatography from native commercial AAG, a mixture of almost equal proportions of the F1, S and A variants, was studied by equilibrium dialysis. A selective binding of disopyramide and methadone to the A variant and a preferential binding of dipyridamole to the F1S variant mixture were found. Lignocaine and chlorpromazine had a slight preference for binding to the A variant and to the F1S mixture, respectively, but progesterone showed no selectivity with regard to any of the variants of AAG. The differences in drug-binding demonstrated between the A variant and the F1S mixture confirmed those of a previous study, in which a selective binding of imipramine to the A variant and of warfarin and mifepristone to the F1S mixture have been found. These results indicate specific drug transport roles for each AAG variant, according to its separate genetic origin. The results of control binding experiments performed with (unfractionated) commercial AAG and the series of tested ligands concurred with that for the separate AAG variants, with respect to the proportion of the A variant (27%) and that of the F1 and S variants (73%) in the commercial protein. In addition, disopyramide, methadone, dipyridamole, chlorpromazine, lignocaine and progesterone were used in equilibrium dialysis displacement experiments to study interactions on binding sites labelled with imipramine for the A variant and with warfarin for the F1S variant mixture. The four latter ligands were found to competitively inhibit the binding of warfarin to the F1S variant mixture and all of them that of imipramine to the A variant. The ligands association constants to each AAG variant obtained from such inhibitory experiments were comparable to those determined in the direct binding studies. As the stochlometry of the interactions of the A variant and the F1S variants, respectively, with their specific ligands was approximately one (1), it was concluded that these ligands bind to each of these variants via a single common binding site. These results indicate that the AAG molecule would have for its ligands at least two separate binding sites, showing different specificity and localization, and not one site, as it is generally assumed. The possible pharmacological and clinical consequences of the binding results with the separate AAG variants are discussed.

Binding, Competitive↗

PubMind: literature-based genetic variant extraction and functional annotation using large language models.

Biomedical literature contains extensive functional knowledge on genetic variants, but much remains inaccessible in unstructured text. Existing resources such as ClinVar and HGMD remain limited by coverage, submission bias, update frequency, and sparse annotation. We develop PubMind, an artificial intelligence (AI) framework that uses large language models (LLMs) to triage and extract variant-function-disease associations and supporting evidence from biomedical text. PubMind captures single-nucleotide, copy-number, structural, and gene-fusion variants, and normalizes records to genomic and transcriptomic coordinates. Benchmarking shows >90% accuracy for variant recognition and 99% precision for disease extraction. Applied to >41 million PubMed abstracts and >5 million full-text articles, PubMind generates PubMind-DB, a database of ~1.3 million unique variants with contextual annotations, accessible via web interface and API. Only ~10% of PubMind variants overlap with ClinVar, and >80% of them show concordant pathogenicity labels. PubMind transforms unstructured biomedical text into structured genomic knowledge, advancing variant interpretation for precision medicine.

Large Language Models↗

[Genetic variants of hepatitis C virus in HIV-infected drug users].

The prevalence of genetic variants (subtypes) of hepatitis C virus (HCV) among HIV-infected and noninfected intravenous drug users (IDU) in Russia is studied. HIV and HCV infections spread in the population of IDUs in Russia irrespective of each other. HCV subtypes 1b, 2a, and 3a (35.2, 18.3, and 29.6%, respectively) are the most prevalent in Russia. The profile of HCV subtype distribution in Russia differs from that in Europe; a "domestic" origin of HCV infection among IDUs is suggested. The authors conclude that identification of HCV subtype should be included in the protocol of examination of HIV-infected patients.

Genome, Viral↗

Fractionation of the genetic variants of human alpha 1-acid glycoprotein in the native form by chromatography on an immobilized copper(II) affinity adsorbent. Heterogeneity of the separate variants by isoelectrofocusing and by concanavalin A affinity chromatography.

Fractionation of the three main genetic variants (F1, S and A) of human alpha 1-acid glycoprotein (AAG), in their native (sialylated) form, by chromatography on immobilized copper(II) affinity adsorbent was investigated. This chromatographic method had been previously developed to fractionate the desialylated protein variants. For that purpose, the three main AAG phenotypes samples (F1S/A, F1/A and S/A), which had been previously isolated from individual human plasma samples, and an AAG sample from commercial source (a mixture of the phenotypes) were used in the native form. Affinity chromatography of these different samples on an iminodiacetate Sepharose-copper(II) gel at pH 7 resolved two protein peaks, irrespective of the origin of the native AAG sample used. The unbound peak 1 was found to consist of the F1, the S or both variants, depending on the phenotype of the AAG sample used in the chromatography. The bound peak 2 was found to consist of the A variant in a pure form. The fractionation results obtained with native AAG were found to be the same as those originally yielded by the desialylated protein. However, comparison of the interactions of native and desialylated AAG with immobilized copper(II) ions, using an affinity chromatographic method and a non-chromatographic equilibrium binding technique, respectively, showed that desialylation increased the non-specific interactions of the protein with immobilized copper(II) ions. The AAG variants were not fractionated when affinity chromatography was performed using immobilized zinc, nickel or cobalt(II) ions, instead of copper. After purification of each variant in the sialylated form (F1, S and A), their respective heterogeneity was studied by analytical isoelectrofocusing with carrier ampholytes in the pH range 2.5-4.5. In addition, the lectin-binding behaviour of the separate sialylated AAG variants was investigated by affinity chromatography on immobilized concanavalin A.

Adsorption↗

Immunological and structural relatedness of isozymes and genetic variants of 3-phosphoglycerate kinase from the mouse.

Isozymes (PGK-1 and PGK-2) and genetic variants (PGK-2A, PGK-2B, and PGK-2C) of 3-phosphoglycerate kinase were purified by affinity chromatography using an 8-(6-aminohexyl)-amino-ATP-Sepharose column as the key step. Antisera raised against purified PGK-1 and PGK-2A were tested for specificity and cross-reactivity by application of double immunodiffusion and enzyme immunoinactivation methods. By double immunodiffusion, no precipitin lines were observed between anti-PGK-2A and PGK-1, but a weak cross-reactivity between anti-PGK-1 and PGK-2A was detected. In addition to specific inhibition of PGK-1 and PGK-2A by their respective antisera, anti-PGK-1 was shown to inhibit PGK-2 activity at high antiserum concentrations, whereas no inhibition of PGK-1 activity by anti-PGK-2A was observed. The amino acid compositions of PGK-1 and PGK-2 revealed a certain degree of homology. However, tryptic peptide maps showed no obvious similarity in the peptide spots between these two 3-phosphoglycerate kinase isozymes. Three electrophoretic variants of PGK-2 were compared biochemically and immunologically. PGK-2C from C57L/J mice, a low activity variant, was shown to be the result of a structural gene mutation that affects the active site of the enzyme.

Amino Acids↗

Human albumin genetic variants: an attempt at a classification of European allotypes.

The relative mobility of albumin and proalbumin genetic variants was estimated by means of cellulose acetate electrophoresis performed with three buffer systems at different pH (8.6, 5.0, and 6.9) after addition of a reference protein and dilution of sera. Numerous experiments using samples of reference variants corroborated the accuracy and reproducibility of this technique. The estimation of the variants' relative mobility at three pH allowed us to distinguish three fast-moving variants (Gent, Vanves, and Reading) and five slow-moving variants (Sondrio, Roma, Christchurch, Lille, and B) in the French population. The frequency of alloalbuminemia in this population is .0004 and is characterized by the high occurrence of albumin B and of the two proalbumin variants, Christchurch and Lille. In order to classify the variants of European origin, the methodology that we developed, owing to its more resolutive possibilities, should be employed as a first step in their identification until establishment of a structural nomenclature making mention of the amino acid substitution characterizing each variant.

Albumins↗

Heterogeneous effects of genetic variants and traits associated with fasting insulin on cardiometabolic outcomes.

Elevated fasting insulin levels (FI), indicative of altered insulin secretion and sensitivity, may precede type 2 diabetes (T2D) and cardiovascular disease onset. In this study, we group FI-associated genetic variants based on their genetic and phenotypic similarities and identify seven clusters with distinct mechanisms contributing to elevated FI levels. Clusters fall into two types: "non-diabetogenic hyperinsulinemia," where clusters are not associated with increased T2D risk, and "diabetogenic hyperinsulinemia," where T2D associations are driven by body fat distribution, liver function, circulating lipids, or inflammation. In over 1.1 million multi-ancestry individuals, we demonstrated that diabetogenic hyperinsulinemia cluster-specific polygenic scores exhibit varying risks for cardiovascular conditions, including coronary artery disease, myocardial infarction (MI), and stroke. Notably, the visceral adiposity cluster shows sex-specific effects for MI risk in males without T2D. This study underscores processes that decouple elevated FI levels from T2D and cardiovascular risk, offering new avenues for investigating process-specific pathways of disease.

Humans↗

Genetic variants in the tumor necrosis factor receptor II gene in patients with multiple sclerosis.

Common genetic variants have been shown to influence disease susceptibility, disease course, or both in multiple sclerosis (MS). Several studies have suggested a role for tumor necrosis factor-alpha (TNF-alpha) in the pathogenesis of MS. Recently, it has been reported that the TNF receptor (TNFR) II plays an essential role in the pathology and progression of experimental autoimmune encephalomyelitis, an animal model of MS. To investigate whether TNFR II polymorphisms influence susceptibility and/or clinical progression of MS, genomic DNA of 321 samples of the Austrian Genetics in MS study group and DNA of 174 platelet donors, who served as healthy controls, were genotyped for five polymorphic sites in the TNFR II gene: exon 6 nucleotide (nt) 676*T-->G, exon 6 nt 783*G-->A (both are associated with non-conserved amino acid substitution), exon 10 nt 1663*G-->A, exon 10 nt 1668*T-->G, and exon 10 nt 1690*T-->C (all of which are located in the 3' non-coding region of the gene). We found a significant association between exon 10 nt 1668*T-->G polymorphism and susceptibility to MS. The other investigated nucleotide substitutions were not associated with susceptibility to or clinical parameters in MS.

Adult↗

Mapping Focal and Generalized Effects of Common Genetic Variants on Human Brain Structure.

Genome-wide association studies (GWAS) have advanced the quest to understand how specific genetic variants influence human brain structure and function. Recent work has identified hundreds of common variants associated with subcortical brain volumes, sparking interest in how these genetic markers overlap across brain networks. While this can be estimated by hierarchical clustering of the genetic correlation matrix to identify modular patterns of shared architecture, no brain-wide maps of these effects are available. To address this, we computed polygenic scores (PGS) from loci associated with ten brain volume regions of interest (ROIs): nine major subcortical structures and intracranial volume, with each locus weighted by its association with regional volume. In an independent sample from the discovery GWAS, we performed large-scale segmentation of 3D volumetric T1-weighted MRI scans using voxel-based morphometry (VBM) to map 3D profile of regions where gray matter volume (GMV) was associated with each PGS. We found statistically significant, localized effects for PGS defined for the amygdala, thalamus, and basal ganglia, but PGS for brainstem volume was associated with widespread differences throughout the brain. These brain-wide maps reveal patterns consistent with both localized and distributed genetic influences, offering a novel approach to interpret the genomic architecture of brain structure.

GWAS↗

SNPannotator: automated functional annotation of genetic variants and linked proxies.

SUMMARY: Genome-wide association studies (GWASs) have identified thousands of genetic variants associated with complex traits and diseases. However, explaining the mechanisms underlying phenotypic variation remains challenging. Here, we introduce SNPannotator, an automated post-GWAS analysis software package designed to streamline the interpretation of GWAS findings. Our pipeline implements a multi-step process that identifies proxy variants in high linkage disequilibrium (LD) with associated lead variants, then queries comprehensive resources (including Ensembl, the GTEx Portal, the eQTL Catalog, and STRING DB) for genomic position, deleteriousness, regulatory annotations, clinical significance, trait associations, expression (eQTLs) and splicing quantitative trait loci (sQTLs), and functional enrichment analyses and compiles the results into user-friendly reports. This package is implemented in the R programming language and includes auxiliary functions for variant lookup and LD exploration. SNPannotator provides a practical framework for efficiently deriving biologically meaningful insights from GWAS data and for assisting researchers in prioritizing candidate variants for functional validation. AVAILABILITY AND IMPLEMENTATION: The SNPannotator package is available from the Comprehensive R Archive Network (CRAN) at https://cran.r-project.org/web/packages/SNPannotator. The development version and tutorial is available on GitHub (https://github.com/omicslaboratory/SNPannotator). The online version of the package is available at https://omicslab.org/snpannotator.

Software↗