SEARCH · PubMed Health

Results for “Variant interpretation”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

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

At least 379 records · Page 21Linked to original sources

PubMed2007

The PROTICdb database for 2-DE proteomics.

PROTICdb is a web-based database mainly designed to store and analyze plant proteome data obtained by 2D polyacrylamide gel electrophoresis (2D PAGE) and mass spectrometry (MS). The goals of PROTICdb are (1) to store, track, and query information related to proteomic experiments, i.e., from tissue sampling to protein identification and quantitative measurements; and (2) to integrate information from the user's own expertise and other sources into a knowledge base, used to support data interpretation (e.g., for the determination of allelic variants or products of posttranslational modifications). Data insertion into the relational database of PROTICdb is achieved either by uploading outputs from Mélanie, PDQuest, IM2d, ImageMaster(tm) 2D Platinum v5.0, Progenesis, Sequest, MS-Fit, and Mascot software, or by filling in web forms (experimental design and methods). 2D PAGE-annotated maps can be displayed, queried, and compared through the GelBrowser. Quantitative data can be easily exported in a tabulated format for statistical analyses with any third-party software. PROTICdb is based on the Oracle or the PostgreSQLDataBase Management System (DBMS) and is freely available upon request at http://cms.moulon.inra.fr/content/view/14/44/.

Databases, Protein↗

PubMed2026

CHEK2 Germline Variants in Cancer Predisposition: Whole Genome Sequencing Results.

While pathogenic germline CHEK2 variants are known to increase cancer risk, there is currently insufficient evidence regarding the precise risk of developing malignant neoplasms associated with specific missense variants or variants of uncertain significance. As a result, no clear clinical guidelines exist regarding consultation, monitoring and specific treatment options for those patients. For the first time in Russia, clinical data and whole-genome sequencing (WGS) results were analyzed for 3150 patients with cancer and suspected hereditary cancer syndromes (HCS) and 5163 healthy individuals. This dataset formed the basis for assessing the role of germline CHEK2 variants in the development of different cancer types. The chromosomal coordinates and coding sequence coordinates are given in accordance with the GRCh38 (hg38) genome assembly and the NM_007194.4 transcript. Pathogenic (P) and likely pathogenic (LP) variants of CHEK2 significantly increased the risk of breast cancer (OR = 2.015 [95% CI: 1.27-3.21]; p = 0.0031), but the association with colorectal cancer was not statistically significant (OR = 1.354 [95% CI: 0.42-4.42]; p = 0.616). A moderate increase in cancer risk was identified for the c.1100del variant (OR = 2.263 [95% CI: 1.19-4.32]; p = 0.0132) and for the common P/LP variants c.1100del, c.444+1G>A and c.433C>T (OR = 2.219 [95% CI: 1.40-3.51]; p = 0.0007). Notably, our study confirmed that CHEK2 c.470T>C (p.Ile157Thr) is the most common variant in the patient group, identified in 3.8% of cases (120/3150), compared with 3.0% in the control group (155/5163). Although the association between the most common CHEK2 variant c.470T>C and cancer risk reached nominal statistical significance (OR = 1.279 [95% CI: 1.00-1.63]; p = 0.0463), the effect size was minimal, suggesting that the contribution of this variant to hereditary cancer risk in the Russian population is modest. Additional studies are required before this variant can be definitively excluded from clinical interpretation.

Humans↗

PubMed2001

Length variation in HV2 of the human mitochondrial DNA control region.

Hair samples were typed from three individuals who exhibited length heteroplasmy in the homopolymeric cytosine stretches (C-stretch) in hypervariable region 2 (HV2). The study demonstrated that for different hairs within an individual, the HV2 C-stretch region can vary with respect to the number of cytosines and/or proportion of C-stretch length variants. Length heteroplasmy may occur regardless of the prominent length variant present in this region. Differences in the number of cytosines at the C-stretch region, or a variation in the relative amounts of heteroplasmic length variants, cannot be used to support an interpretation of exclusion.

Amino Acid Sequence↗

PubMed2002

[Diagnostic and therapeutic problems in adult onset Still's disease (data of a long-term follow-up)].

15 patients with Still's disease of adults (SDA) were followed up for 17 years maximum. The disease showed a principal clinical-laboratory syndrome observed both in SDA debut and exacerbations (recurrences). Clinical manifestations of SDA do not arise stereotypically causing difficulties in its nosological interpretation. SDA course is represented by three variants: monophasic (monocyclic), recurrent and chronic persisting with development of destructive arthritis. Use of nonsteroid antiinflammatory drugs is analysed, indications to administration of glucocorticoids and basic treatment are listed. Reversibility of systemic SDA manifestations except the articular one is shown. About half of the patients develop chronic destructive arthritis. In active SDA, renal amyloidosis and chronic renal failure may develop with lethal outcome.

Adolescent↗

PubMed1990

[Cellular immunity in pollinosis patients].

A study of 107 patients with pollinosis with exacerbation during the spring-summer season revealed T-lymphopenia, increased number of 0-lymphocytes, reduction of the level of "active" and theophyllin-sensitive lymphocytes and histamin-sensitive cells. The number of low-differentiated B-cells increased, the number of autorosette-forming lymphocytes decreased. The revealed changes may be interpreted as secondary immunological insufficiency (relative hyposuppressor variant).

Adolescent↗

PubMed1989

[Clinically conditional variants of the immune response in viral hepatitis A and B in children].

The immunity characteristics of the T-, B- and A-systems have been studied on the basis of the data registered in the dynamics of the acute period of the disease and several times in catamnesis during 6-12 months of the convalescence period in 217 children with viral hepatitis A and 99 children with viral hepatitis B. The clinical course of viral hepatitis A and that of viral hepatitis B have been found to have certain parallels in their development, as well as specific features of immune response, which can be subdivided into 3 main groups: (a) immunological imbalance, (b) the phase of immunodepression and (c) secondary immunodeficiency. The distinguishing of the variants of immune response and their clinical interpretation are of practical importance for the early prognostication of the course and outcome of the processes and for the differentiated approach to the treatment of viral hepatitides in children.

Adolescent↗

PubMed2025

Missense variants pathogenicity annotation from homologous proteins.

MOTIVATION: High-throughput DNA sequencing has revealed millions of single nucleotide variants (SNVs) in the human genome, with a small fraction linked to disease. The effect of missense variants, which alter the protein sequence, is particularly challenging to interpret due to the scarcity of clinical annotations and experimental information. While using conservation and structural information, current prediction tools still struggle to predict variant pathogenicity. In this study, we explored the pathogenicity of homologous missense variants-variants in equivalent positions across homologous proteins-focusing on proteins involved in autosomal dominant diseases. RESULTS: Our analysis of 2976 pathogenic and 17 555 non-pathogenic homologous variants demonstrated that pathogenicity can be extrapolated with 95% accuracy within a family, or up to 98% for closer homologs. Remarkably, the evaluation of 27 commonly used mutation predictor methods revealed that they were not fully capturing this biological feature. To facilitate the exploration of homologous variants, we created HomolVar, a web server that computationally predicts the pathogenesis of missense variants using annotations from homologous variants, freely available at https://rarevariants.org/HomolVar. Overall, these findings and the accompanying tool offer a robust method for predicting the pathogenicity of unannotated variants, enhancing genotype-phenotype correlations, and contributing to diagnosing rare genetic disorders. AVAILABILITY AND IMPLEMENTATION: HomolVar is freely available at https://rarevariants.org/HomolVar.

Mutation, Missense↗

PubMed2025

Optical genome mapping improves clinical interpretation of constitutional copy-number gains and reduces their VUS burden.

PURPOSE: Genomic structure of copy-number gains is critical for their clinical interpretation but cannot be determined by chromosomal microarray (CMA) analysis, which does not provide information about chromosomal location and orientation of multiplied regions. We thus hypothesized that in CMA testing gains have higher probability than losses to be classified as variants of uncertain significance (VUS) and that structural information from optical genome mapping (OGM) may improve their interpretation. METHODS: Using a χ2 test, we assessed the association between classification of copy-number variants as VUS and their type (gains vs losses) in a cohort of 4073 CMA cases. Thirty-three VUS gains involving disease-associated genes were characterized by OGM to evaluate if OGM data enable their more conclusive clinical interpretation. RESULTS: The proportion of variants reported as VUS compared with likely pathogenic/pathogenic was significantly higher for gains than losses, confirming their increased VUS burden. OGM successfully determined genomic structure for all 33 copy-number gains, showing that 26 of 33 were tandem duplications and 7 of 33 were complex rearrangements. Structural information facilitated clinical interpretation in majority of the cases; it supported benign nature for 27 of 33 gains and was inconclusive or supported pathogenic role for 6 of 33. An estimated 20% of reported VUS gains would not have been reportable if we had OGM data. CONCLUSION: We illustrate a specific advantage of OGM compared with CMA: in addition to detecting both copy-number variants and balanced rearrangements, OGM improves clinical interpretation of copy-number gains by providing structural information and is thus expected to significantly decrease their VUS burden.

Humans↗

PubMed1998

Association of hypertension with T594M mutation in beta subunit of epithelial sodium channels in black people resident in London.

BACKGROUND: Liddle's syndrome is a rare inherited form of hypertension in which mutations of the epithelial sodium channel result in increased renal sodium reabsorption. Essential hypertension in black patients also shows clinical features of sodium retention so we screened black people for the T594M mutation, the most commonly identified sodium-channel mutation. METHODS: In a case-control study, 206 hypertensive (mean age 48.0 [SD 11.8] years, men:women 80:126) and 142 normotensive (48.7 [7.4] years; 61:81) black people who lived in London, UK, were screened for T594M. Part of the last exon of the epithelial sodium-channel beta subunit from genomic DNA was amplified by PCR. The T594M variant was detected by single-strand conformational polymorphism analysis of PCR products and confirmed by DNA sequencing. FINDINGS: 17 (8.3%) of 206 hypertensive participants compared with three (2.1%) of 142 normotensive participants possessed the T594M variant (odds ratio [OR]=4.17 [95% CI 1.12-18.25], p=0.029). A high proportion of participants with the T594M variant were women (15 of 17 hypertensive participants and all three normotensive participants), whereas women comprised a lower proportion of the individuals screened (61.2% hypertensive, 57.7% normotensive). However, the association between the T594M variant and hypertension persisted after adjustment for sex and body-mass index (Mantel-Haenszel OR=5.52 [1.40-30.61], p=0.012). Plasma renin activity was significantly lower in 13 hypertensive participants with the T594M variant (median=0.19 ng mL(-1) h(-1)) than in 39 untreated hypertensive individuals without the variant (median=0.45 ng mL(-1) h(-1), p=0.009). INTERPRETATION: Among black London people the T594M sodium-channel beta subunit mutation occurs more frequently in people with hypertension than those without. The T594M variant may increase sodium-channel activity and could raise blood pressure in affected people by increasing renal tubular sodium reabsorption. These findings suggest that the T594M mutation could be the most common secondary cause of essential hypertension in black people identified to date.

Black People↗

PubMed1969

Hemoglobin NYU, a delta chain variant, alpha 2 delta 2 lys.

A minor hemoglobin (Hb) component with the electrophoretic properties of the delta-chain variant Hb A(2') was encountered in two unrelated families of Russian-Jewish ancestry. This minor component, designated Hb NYU, was shown to result from the substitution of lysine for asparagine at delta(12). We have confirmed studies of others that hemoglobin A(2') isolated from the hemoglobin of some African subjects, results from the replacement of the normal glycine at delta(16) by arginine. Thus for interpretations of the incidence of delta-chain variants in different populations, electrophoretic data are not sufficient. In members of one of the families in the present study, the visual estimations of normal Hb A(2) and of Hb NYU on starch-gel electrophoretic patterns suggested the presence of delta-thalassemia. In hemolysates of one of the heterozygotes for Hb NYU, hemoglobin A(2) was not demonstrable with starch-gel electrophoretic methods but was readily recovered by column chromatography in approximately the amounts expected for delta-chain heterozygotes.

Adolescent↗

PubMed2003

Haemoglobin Marseille-Long Island and interpretation of HbA1c: which HbA1c result is the "right answer"?

A woman was screened for diabetes using glycated haemoglobin (HbA1c). Vastly different results were obtained by high performance liquid chromatography (45%), immunoassay (2.9%), and affinity chromatography (4.2%) compared with the non-diabetic range of less than 6.4%. Mass spectral studies confirmed the presence a haemoglobin variant, haemoglobin Marseille-Long Island which had confounded interpretation by all methods.

Adult↗

PubMed2026

Mutation rate heterogeneity biases variant effect prediction and reveals genuine mutational robustness.

Variant effect predictors (VEPs) are widely used to interpret the functional consequences of human genetic variation. Because most methods rely on sequence conservation, they implicitly treat conservation as evidence of functional constraint. However, substitution patterns across a phylogeny reflect not only selection but also differences in underlying mutation rates. Here, we show that this creates a systematic confounding: most VEPs capture mutation rate variation and misinterpret it as variation in functional importance. Widely used conservation metrics exhibit a related bias; in particular, phyloP scores correlate strongly with mutation rate even at putatively neutral sites. Consequently, variants at low-mutation-rate sites tend to be predicted as more damaging, and variants at highly mutable sites as more tolerated, than warranted by their true functional impact. We also identify a distinct biological signal in experimental measurements of mutational effects on protein stability: amino acid substitutions that are more likely to arise are, on average, less destabilizing than rarer substitutions. This provides empirical support for mutational robustness in the context of protein stability. However, this relationship is insufficient to explain the mutation-rate dependence observed in current VEP outputs. Together, our findings show that mutation rate heterogeneity systematically biases current variant effect prediction frameworks, highlight the need to model mutation probabilities explicitly in future VEPs, and reveal a genuine biological signal of mutational robustness.

conservation scores↗

PubMed2026

Potential Contribution of DES (p.Leu88Met) and MYH7 (p.Arg787His) Variants to Familial Restrictive Cardiomyopathy.

BACKGROUND: Restrictive cardiomyopathy (RCM) is a rare, severe cardiac disease with a heterogeneous genetic basis. Both genetic and nongenetic factors contribute to RCM pathogenesis. Identifying the underlying molecular causes is important for diagnosis and family screening. In this study, we investigated the genetic basis of RCM in a 52-year-old woman with a family history of RCM and heart disease. METHODS: Genetic predisposition was evaluated using whole-exome sequencing (WES). Candidate variants identified in the proband were validated by Sanger sequencing and interpreted using bioinformatics tools and the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) guidelines. RESULTS: Two heterozygous missense variants were identified: a novel DES c.262C > A (p.Leu88Met) variant and a previously reported MYH7 c.2360G > A (p.Arg787His) variant. The DES variant was absent from population databases and was classified as a variant of uncertain significance, whereas the MYH7 variant has been reported in the cardiomyopathy spectrum, primarily in hypertrophic cardiomyopathy. Although both variants may be relevant to the participant's phenotype, their contribution remains uncertain without segregation and functional studies. CONCLUSION: These findings expand the spectrum of DES and MYH7 variants observed in cardiomyopathy and highlight the need for further segregation and functional analyses to clarify their clinical significance in RCM. Identifying the genetic basis of RCM in this family may improve screening strategies and guide clinical management.

DES↗

PubMed2003

Ethnic differences in cardiac potassium channel variants: implications for genetic susceptibility to sudden cardiac death and genetic testing for congenital long QT syndrome.

OBJECTIVE: To determine the spectrum, frequency, and ethnic-specificity of channel variants in the potassium channel genes implicated in congenital long QT syndrome (LQTS) among healthy subjects. SUBJECTS AND METHODS: Genomic DNA from 744 apparently healthy individuals-305 black, 187 white, 134 Asian, and 118 Hispanic--was subject to a comprehensive mutational analysis of the 4 LQTS-causing potassium channel genes: KCNQ1 (LQT1), KCNH2 (LQT2), KCNE1 (LQT5), and KCNE2 (LQT6). RESULTS: Overall, 49 distinct amino acid-altering variants (36 novel) were identified: KCNQ1 (n = 16), KCNH2 (n = 25),KCNE1 (n = 5), and KCNE2 (n = 3). More than half of these variants (26/49) were found exclusively in black subjects. The known K897T-HERG and the G38S-min K common polymorphisms were identified in all 4 ethnic groups. Excluding these 2 common polymorphisms, 25% of black subjects had at least 1 nonsynonymous potassium channel variant compared with 14% of white subjects (P < .01). CONCLUSIONS: To our knowledge, this study represents the first comprehensive determination of the frequency and spectrum of cardiac channel variants found among healthy subjects from 4 major ethnic groups. Defining the population burden of genetic variants in these critical cardiac ion channels is crucial for proper interpretation of genetic test results of individuals at risk for LQTS. This compendium provides a resource for epidemiological and functional investigation of variant effects on the repolarization properties of cardiac tissues, including susceptibility to lethal cardiac arrhythmias.

Alleles↗

PubMed2002

Software for machine-independent quantitative interpretation of SSCP in capillary array electrophoresis (QUISCA).

PCR single-stranded conformational polymorphism (SSCP) analysis is a simple and rapid electrophoretic technique for the sensitive detection of sequence variants of PCR products. Here we describe a cross-platform program package, quantitative interpretation of SSCP in capillary array (QUISCA), which allows semi-automated quantitative detection of sequence variants separated by multicolor fluorescence-based SSCP electrophoresis using various capillary array apparatus. The program, together with the QUISCAview as a graphical user interface, takes trace data in ASCII format and processes them with three modules: signal denoising/baseline subtraction, color-matrix construction/application, and calibration of peak positions between multiple capillary runs using internal standard peaks. QUISCA is compatible with data from various widely used capillary array sequencers and is suitable not only for finding or typing SNPs in individual DNAs but also for the accurate estimation of the allele frequencies of many SNPs using a pooled DNA strategy. QUISCA can also serve as a versatile core program for various fragment analyses.

Algorithms↗

PubMed1997

Susceptibility to HIV infection and progression of AIDS in relation to variant alleles of mannose-binding lectin.

BACKGROUND: Low serum concentrations of mannose-binding lectin (MBL) are associated with increased susceptibility to recurrent infection. Three variant alleles in the MBL gene (B, C, and D), cause low serum concentrations of the protein. We investigated whether variant alleles of MBL affect susceptibility to infection with HIV and progression of AIDS. METHODS: Between 1983 and 1986, all men who attended two clinics in Copenhagen for HIV screening were invited to take part in our study. We investigated the prevalence of variant alleles of MBL (detected by PCR) and assessed the prognostic value of these alleles and the corresponding serum MBL concentrations (measured by ELISA) in 96 homosexual men with HIV infection and in two control groups (123 healthy adults and 36 HIV-negative homosexual men at high risk of HIV infection because of their sexual behaviour). Follow-up was for up to 10 years. FINDINGS: Eight (8%) of the HIV-infected men were homozygous for the variant MBL alleles compared with one (0.8%) of the healthy controls (p = 0.005) and none of the high-risk homosexual controls (p = 0.05). We found no significant association between MBL genotype and time from first positive HIV test to progression of AIDS (p = 0.8). However, in the 61 HIV-infected men who developed AIDS, the median survival time was significantly shorter after the AIDS diagnosis for men who were carriers of the variant alleles (both homozygous and heterozygous) than for men homozygous for the normal MBL allele (11 [IQR 4-21] vs 18 months [9-44], p = 0.007). Among men who developed AIDS, there was a significant difference in survival time between those with serum MBL concentrations below the lower quartile, those within the IQR, and those above the upper quartile (p = 0.02). Multivariate analysis showed that men who developed AIDS and had low serum MBL concentrations had an increased rate of rapid death, independently of CD4 T-cell counts at AIDS diagnosis. INTERPRETATION: Our findings suggest that homozygous carriers of variant MBL alleles are at increased risk of HIV infection, either directly or indirectly because of increased susceptibility to coinfections. These alleles are also associated with a significantly shorter survival time after a diagnosis of AIDS.

Acquired Immunodeficiency Syndrome↗

PubMed2025

Multiple Psychiatric Traits Enriched for Brain Tissues in the Early Postpartum Period.

BACKGROUND: The perinatal period is a high-risk time for onset of various psychiatric disorders. However, it is unclear how genetic risk factors for these disorders interact with biological changes associated with pregnancy and postpartum. This study evaluates whether psychiatric genome-wide association study (GWAS) results are enriched within various brain regions across the perinatal period. METHODS: Tissue-specific enrichment analyses were conducted to estimate the potential impact of GWAS loci on transcriptional changes in the brain across the perinatal period. GWAS summary statistics were obtained for 26 psychiatric phenotypes. RNA-sequencing data was acquired from four brain regions (hypothalamus, hippocampus, cerebellum, and neocortex) in mice at six timepoints (virgin, 14- and 16-days post-conception, and 1-, 3- and 10-days postpartum). RESULTS: Hippocampus and neocortex in the early postpartum period are significantly enriched (q-value < 0.05) for genetic variants associated with schizophrenia (SCZ), bipolar disorder (BD), depressive symptoms, and major depressive disorder with suicidal features. The most significant enrichment occurred in the neocortex for SCZ and BD, peaking at postpartum day 1 (SCZ p-value = 3.85 × 10-8; BD p-value = 6.65 × 10-5). In the hippocampus, BD and SCZ were enriched at postpartum day 1 (SCZ p-value = 3.27 × 10-3; BD p-value = 4.33 × 10-3). No enrichment was observed in cerebellum or hypothalamus for any of the psychiatric traits tested. CONCLUSIONS: The results accord with previous epidemiological studies and provide context in which to interpret GWAS results. Understanding the burden of genetic variants across the perinatal period may help prioritise pathways underlying onset of psychiatric disorders outside of pregnancy and postpartum periods.

Journal Article↗

PubMed1986

Binocular depth mixture: an artefact of eye vergence?

Several studies by Foley et al. suggest that for particular stereoscopic stimulus conditions perceived depth depends on the luminance ratios of the stimuli. Perceived depth appears "shifted" in the direction of the most luminant stimulus. This finding has been interpreted as contradictory evidence against modern neuronal network or algorithmic models which are extensions or variants of so-called projection theories of stereopsis. The present study shows that this interpretation lacks a solid basis and that the apparent depth shift effect probably qualifies as an artefact caused by systematic fixation errors (fixation disparities). With a psychophysical methodology which aims at preventing the occurrence of systematic fixation errors no depth shift effect is found.

Adult↗