index int64 0 99 | name stringlengths 11 79 | category stringclasses 7
values | input stringlengths 28 313 | expected stringlengths 12 267 |
|---|---|---|---|---|
0 | Gene for NM_001045477.4:c.187C>T | Gene and Variant Utilities | What gene is primarily associated with the variant NM_001045477.4:c.187C>T? | The genes associated include NUTM2G. |
1 | Protein change for NM_001045477.4:c.187C>T | Gene and Variant Utilities | What is the protein change resulting from NM_001045477.4:c.187C>T? | The protein change is p.P63S. |
2 | NUTM2G OMIM entries | Gene-Phenotype Databases | Does NUTM2G have any entries in OMIM database? | NUTM2G has no OMIM match and no known Mendelian phenotypes. |
3 | MECP2 OMIM entries | Gene-Phenotype Databases | Does MECP2 have an OMIM number? | Yes, MECP2's OMIM number is 300005. |
4 | MECP2 OMIM entries 2 | Gene-Phenotype Databases | Does MECP2 have any associated Mendelian phenotypes? | MECP2 is linked with several Mendelian phenotypes (generally: autism susceptibility and intellectual developmental disorders). |
5 | Average dbNSFP rank score | Variant Prioritization | What is the average dbNSFP rank score for p.P63S in NUTM2G? | The average dbNSFP rank score is 0.214. |
6 | CADD phred score | Variant Prioritization | What is the CADD phred score for the variant NM_001045477.4:c.187C>T? | CADD phred score is 8.103. |
7 | CADD phred prediction | Variant Prioritization | What is the CADD phred prediction for the variant rs137852987? | The CADD prediction for this variant is highly deleterious. |
8 | REVEL prediction | Variant Prioritization | Tell me about the variant NM_001045477.4:c.187C>T. According to REVEL, how is this variant classified? | REVEL predicts it with a score of 0.027, meaning lower pathogenicity. |
9 | PolyPhen-2 prediction | Variant Prioritization | According to PolyPhen-2, how is NM_001045477.4:c.187C>T predicted? | PolyPhen-2 HumDiv and HumVar both classify it as 'Benign'. |
10 | ClinVar records for NUTM2G | Variant Prioritization | How many ClinVar variants are associated with NUTM2G? | Yes, NUTM2G has 99 reported variants in ClinVar. |
11 | ClinVar pathogenic allele count | Variant Prioritization | How many NUTM2G variants are reported as pathogenic (not likely pathogenic) in ClinVar? | 33 alleles are reported as pathogenic. |
12 | ClinVar likely pathogenic variant count | Variant Prioritization | How many NUTM2G variants are reported as likely pathogenic in ClinVar? | 3 alleles are reported as likely pathogenic. |
13 | gnomAD presence | Variant Prioritization | Is Chr9:99694174 C>T found in gnomAD? | This variant is not found in gnomAD control populations. |
14 | gnomAD presence 2 | Variant Prioritization | Is Chr6:99365567 T>C (hg19) found in gnomAD? Perform a liftover if needed. | Yes, this variant is found in gnomAD control populations. |
15 | LoF o/e score | Variant Prioritization | What is the LoF o/e (loss-of-function observed/expected) score for NUTM2G? | The LoF o/e score is 0.84 |
16 | LoF o/e implication | Variant Prioritization | What does the LoF o/e score imply about the strength of selection on NUTM2G? | NUTM2G is not under strong selection against loss-of-function alleles. |
17 | DGV entries | Variant Prioritization | Are there any DGV entries for NUTM2G? If so, how many? | Yes, there are 16 DGV entries for NUTM2G. |
18 | DECIPHER control variants | Variant Prioritization | Are there any DECIPHER control variants involving NUTM2G? | Yes, there is 1 control individual with a duplication containing NUTM2G. |
19 | DIOPT ortholog mouse | Ortholog Data | What is the gene symbol for the DIOPT ortholog of NUTM2G in mouse? | The mouse ortholog is Nutm2. |
20 | DIOPT ortholog rat | Ortholog Data | What is the gene symbol for the DIOPT ortholog of NUTM2G in rat? | The rat ortholog is Nutm2f. |
21 | DIOPT ortholog fly | Ortholog Data | What is the gene symbol for the DIOPT ortholog of NUTM2G in fly? | There is no clear ortholog of NUTM2G in fly. |
22 | Highest GTEx expression | Expression Databases | Which tissue shows the highest expression of NUTM2G in the GTEx? | Highest expression is observed in the testis. |
23 | Protein domain | Gene and Variant Utilities | What type of protein domain does NUTM2G contain? | It contains an Nuclear protein in Testes family protein domain. |
24 | Drugs or ligands | Gene and Variant Utilities | Are there any approved drugs or active ligands targeting NUTM2G? | No approved drugs or active ligands were found for NUTM2G. |
25 | Geno2MP by entrez id value comparison | Gene-Phenotype Databases | What is the most common mutation category in ENSG00000197386 gene variant HPO entries? | Synonymous/Unknown |
26 | Geno2MP by entrez id | Gene-Phenotype Databases | How many noncoding HTT gene variant HPO entries are there in the Geno2MP database? | 654 HPO entries for noncoding HTT variants |
27 | OMIM by disease name | Gene-Phenotype Databases | Which gene is most associated with Huntington's disease? | The gene most associated with Huntington's is HTT |
28 | Omim by mim number | Gene-Phenotype Databases | Which genes are connected to mim number 114480? | The genes connected include BRCA1, BRCA2, RAD51C, and RAD51D |
29 | Omim by variant - variant does not exist | Gene-Phenotype Databases | Is the variant chr2-74558644-C-T present on OMIM? If so, what is that associated phenotype? | The variant is not present on OMIM. |
30 | Omim by variant | Gene-Phenotype Databases | Is the HGVS variant chr4:3160307 C>T listed in OMIM? If so, what is the associated phenotype? | The associated phenotype is Lopes-Maciel-Rodan syndrome. |
31 | HPO by phenotype query | Gene-Phenotype Databases | What HPO terms are associated with the search term 'hemolytic anemia'? | HP:0001878, HP:0001890, HP:0004804 are among the results |
32 | HPO by id query | Gene-Phenotype Databases | How many genes are associated with HPO term HP:0002671 | HP:0002671 is associated with 59 genes. |
33 | UniProt ID and name | Gene and Variant Utilities | What is the UniProt ID and protein name associated with NUTM2G? | UniProt ID Q5VZR2, and the protein name is NUT family member 2G. |
34 | GO functions for TP53 | Gene and Variant Utilities | Regarding GO molecular functions, does the fly ortholog for TP53 have RNA Polymerase II TF binding function? | Yes, the fly ortholog of TP53 has the molecular function "RNA polymerase II transcription factor binding" (GO:0001085). |
35 | Ortholog tissue expression | Expression Databases | For the human gene HTT, which mouse developmental stage has the most ortholog expression annotations? | Embryo stage |
36 | PubMed search by gene name | Literature | Search PubMed for articles about BRCA1. How many articles are there? | At least 24,721 articles about BRCA1 are found. |
37 | PubMed search by disease name | Literature | Search PubMed for articles about Rett syndrome. Limit to 3 results and provide PMIDs and abstracts. | No more than 3 articles are found, all are about Rett syndrome and include PubMed ids [37628658, 7620591, 39331775]. |
38 | PMC abstract lookup by PMC ID | Literature | Get the abstract for PMC article PMC3518823. | Abstract text is retrieved. |
39 | PMC full text lookup by PMC ID | Literature | Get the full text for PMC article PMC3518823. | Full text is retrieved with more content than just the abstract. |
40 | PMC table count | Literature | How many tables are in the PMC article with PMID 23248578? | There are 2 tables in this article. |
41 | PMC figure captions | Literature | What are the figure captions in PMC article PMC3518823? | Figure captions are listed. |
42 | STRING list all protein interactions | Protein Interactions | What is the gene symbol(s) for the protein(s) connected to NUTM2G on STRING? | NUTM2G is connected to VIRMA on STRING. |
43 | STRING check for existing protein interaction | Protein Interactions | Is there an interaction between MAP3K1 and HRAS in STRING? | Yes, there is an interaction between these two genes in STRING. |
44 | STRING check for nonexistent protein interaction | Protein Interactions | Is there an interaction between MAP3K1 and NUTM2G in STRING? | No, there is no interaction between these two genes in STRING. |
45 | Gene phenotype association for connected gene and phenotype | Gene-Phenotype Databases | Does TTN gene have an association with dilated cardiomyopathy? | Yes, TTN gene is associated with dilated cardiomyopathy. |
46 | Gene phenotype association for unconnected gene and phenotype | Gene-Phenotype Databases | Is the NUTM2G gene associated with dilated cardiomyopathy? | No, NUTM2G gene is not associated with dilated cardiomyopathy. |
47 | Gene phenotype association for connected gene and phenotype 2 | Gene-Phenotype Databases | Is TTN gene associated with limb-girdle muscular dystrophy? | Yes, TTN gene is associated with limb-girdle muscular dystrophy. |
48 | Gene alias list | Gene and Variant Utilities | What are the known aliases for the NUTM2G gene? | Known aliases for NUTM2G include NUTMG, and FAM22G. |
49 | Gene alias check for existing alias | Gene and Variant Utilities | Is FAM22G an alias for NUTM2G? | Yes, FAM22G is an alias for NUTM2G. |
50 | Gene alias check for nonexistent alias | Gene and Variant Utilities | Is SRC2 an alias for PTPN11? | No, SRC2 is not an alias for PTPN11. |
51 | Full gene name | Gene and Variant Utilities | What is the full name of the gene NUTM2G? | The full name of NUTM2G is NUT family member 2G. |
52 | Full gene name 2 | Gene and Variant Utilities | What is the full name of the gene PTPN11? | The full name of PTPN11 is protein tyrosine phosphatase non-receptor type 11. |
53 | Full gene name 3 | Gene and Variant Utilities | What is the full name of the gene ENSG00000012048? | The full name of ENSG00000012048 is BRCA1 DNA repair associated. |
54 | Use geno2mp to identify HPO terms linked to specific variant | Gene-Phenotype Databases | What narrow HPO terms are associated with the variant chr8:70157018 A>T? | The narrow HPO term associated with this variant includes HP:0010316 (Ebstein's anomaly of the tricuspid valve). |
55 | Use geno2mp to identify HPO terms linked to specific variant 2 | Gene-Phenotype Databases | What HPO terms are associated with the variant chr21:45175759 C>T? | The HPO terms associated with this variant includes HP:0000776 (Congenital diaphragmatic hernia) and HP:0005684 (Distal arthrogryposis). |
56 | Use geno2mp to identify HPO terms linked to specific variant 3 | Gene-Phenotype Databases | What HPO terms are associated with the variant chr12:14841081 C>T? | The HPO terms associated with this variant includes HP:0008058 (Aplasia/Hypoplasia of the optic nerve) and HP:0000501 (Glaucoma). |
57 | Use geno2mp to find number of homozygous cases for a variant 1 | Gene-Phenotype Databases | How many homozygous cases carrying the variant chr8:70126887 C>T are reported in the Geno2MP database? | There are 0 homozygous cases reported with this variant in the Geno2MP database. |
58 | Use geno2mp to find number of heterozygous cases for a variant 2 | Gene-Phenotype Databases | How many heterozygous cases are reported for the variant chr21:45175759 C>T in the Geno2MP database? | There are 3 heterozygous cases reported with this variant in the Geno2MP database. |
59 | Use geno2mp to find number of homozygous and heterozygous cases for a variant 3 | Gene-Phenotype Databases | How many homozygous and heterozygous cases are reported for the variant chr12:14841081 C>T in the Geno2MP database? | There are 0 homozygous and 5 heterozygous cases reported for this variant in the Geno2MP database. |
60 | Explanation of each variant prioritization tool 1 | Variant Prioritization | What is the intuition behind AlphaMissense variant prioritization tool? | AlphaMissense uses protein structure predictions to assess the potential impact of missense variants on protein function. |
61 | Explanation of each variant prioritization tool 2 | Variant Prioritization | What is the intuition behind CADD variant prioritization tool? | CADD integrates multiple annotations into a single score to predict the deleteriousness of variants across the genome. |
62 | Explanation of each variant prioritization tool 3 | Variant Prioritization | What is the intuition behind REVEL variant prioritization tool? | REVEL combines scores from multiple individual tools to improve the accuracy of predicting the pathogenicity of missense variants. |
63 | Explanation of pLI score 1 | Variant Prioritization | What does a pLI score represent in genetic variant interpretation? | A pLI score estimates the probability that a gene is intolerant to loss-of-function variants, with higher scores indicating greater intolerance. |
64 | Explanation of pLI score 2 | Variant Prioritization | How is the pLI score calculated? | The pLI score is calculated based on the observed and expected number of loss-of-function variants in a gene, using population sequencing data. |
65 | Explanation of pLI score 3 | Variant Prioritization | What is the interpretation of pLI score for TTN gene? | The TTN gene has a low pLI score, indicating it is tolerant to loss-of-function variants. |
66 | Get pLI score for gene 1 | Variant Prioritization | What is the pLI score for NUTM2G gene? Provide interpretation. | The pLI score for NUTM2G is 5.629288140820559e-10, indicating it is tolerant to loss-of-function variants. |
67 | Get pLI score for gene 2 | Variant Prioritization | What is the pLI score for MECP2 gene? Provide interpretation. | The pLI score for MECP2 is 0.8938193637798467, indicating it is intolerant to loss-of-function variants. |
68 | Get pLI score for gene 3 | Variant Prioritization | What is the pLI score for TTN gene? Provide interpretation. | The pLI score for TTN is approximately 2.56 * 10^-96, indicating it is tolerant to loss-of-function variants. |
69 | Get pLI score for variant | Variant Prioritization | What is the pLI score for chr21:45175759 C>T? Give for the variant, not the gene as a whole. | I cannot provide pLI scores for specific variants - pLI scores are gene-level metrics. Gene level pLI score may be provided but is not required. |
70 | Explanation of o/e score 1 | Variant Prioritization | What does the o/e (observed/expected) score represent in genetic variant interpretation? | The o/e score estimates the ratio of observed to expected loss-of-function variants in a gene, with lower scores indicating stronger selection against such variants. |
71 | Explanation of o/e score 2 | Variant Prioritization | How is the o/e score calculated? | The o/e score is calculated by comparing the number of observed loss-of-function variants to the number expected based on mutation rates and gene length. |
72 | Explanation of o/e score 3 | Variant Prioritization | What is the interpretation of o/e score for MECP2 gene? | The MECP2 gene has a low o/e score, indicating it is under strong selection against loss-of-function variants. |
73 | Copare pLI and o/e scores for gene 1 | Variant Prioritization | How do the pLI and observed/expected scores for TTN gene compare, and how should they be interpreted? | The pLI score for TTN is 2.56 * 10^-96 (nearly 0), and the o/e (LOEUF) score is 0.327. pLI indicates high tolerance to loss of function, while o/e implies some constraint. |
74 | Compare pLI and o/e scores for gene 2 | Variant Prioritization | How do the pLI and o/e scores for MECP2 gene compare? Provide interpretation. | Both pLI and o/e scores for MECP2 indicate it is intolerant to loss-of-function variants. |
75 | Compare pLI and o/e scores for gene 3 | Variant Prioritization | How do the pLI and o/e scores for CHEK2 gene compare? Provide interpretation. | Both scores indicate tolerance to loss-of-function variants. |
76 | Explain discrepancy between pLI and o/e scores | Variant Prioritization | Why might a gene have a high pLI score but a relatively high o/e score? | A gene might have a high pLI score indicating intolerance to loss-of-function variants, but a relatively high o/e score if there are more observed variants than expected due to factors like differing variant classes, population-specific variants or sequencing errors. |
77 | Descriptions of databases 1 | Variant Prioritization | What is the general purpose of the gnomAD database in genetic research? | gnomAD aggregates and harmonizes exome and genome sequencing data from a variety of large-scale sequencing projects to provide allele frequency information for genetic variants in diverse populations. |
78 | Descriptions of databases 2 | Variant Prioritization | What is the general purpose of the ClinVar database in genetic research? | ClinVar is a public database that aggregates information about genomic variation and its relationship to human health, providing a resource for clinicians and researchers to understand the clinical significance of genetic variants. |
79 | Descriptions of databases 3 | Variant Prioritization | What is the general purpose of the DECIPHER database in genetic research? | DECIPHER is a database that collects and shares genomic and phenotypic data from patients with rare genetic disorders to facilitate diagnosis and research into the genetic basis of these conditions. |
80 | Positive Drugs or ligands 1 | Gene and Variant Utilities | Are there any approved drugs or active ligands targeting MAP3K1? | No approved drugs, two active ligands were found for MAP3K1. |
81 | Positive Drugs or ligands 2 | Gene and Variant Utilities | Are there any approved drugs or active ligands targeting PTPN11? | No approved drugs, ten active ligands targeting PTPN11 were found. |
82 | Positive Drugs or ligands 3 | Gene and Variant Utilities | Are there any approved drugs or active ligands targeting BRCA1? | No approved drugs, four active ligands were found for BRCA1. |
83 | Aditional questions on GO categories (MF, CC, BP) 1 | Gene and Variant Utilities | What biological processes is M1AP involved in according to GO annotations? | M1AP is involved in RNA processing, Meiosis I, Spermatogenesis, Chromatin assembly among others. |
84 | Aditional questions on GO categories (MF, CC, BP) 2 | Gene and Variant Utilities | What cellular components is BRCA1 associated with according to GO annotations? | BRCA1 is associated with cellular components such as the nucleus and DNA repair complexes. |
85 | Aditional questions on GO categories (MF, CC, BP) 3 | Gene and Variant Utilities | What molecular functions does PTPN11 have according to GO annotations? | PTPN11 has molecular functions including protein tyrosine phosphatase activity |
86 | Aditional questions on GO categories (MF, CC, BP) 4 | Gene and Variant Utilities | Does MECP2 have any GO annotations related to transcription regulation? | Yes, MECP2 has GO annotations related to transcription regulation, including transcription. |
87 | Aditional questions on GO categories (MF, CC, BP) 5 | Gene and Variant Utilities | Is TTN associated with any GO annotations related to carbohydrate metabolism? | No, TTN is not associated with GO annotations related to carbohydrate metabolism. |
88 | Ortholog tissue expression 1 | Expression Databases | For the human gene CDKN2A, which cell component has the most ortholog expression annotations in rats? | The nucleus and other components are tied for the most CDKN2A expression annotations in rats. |
89 | Ortholog tissue expression 2 | Expression Databases | For the human gene OR51A2, which tissues have the most ortholog expression annotations in zebrafish? | The chemosensory, sensory and nervous systems have the most OR51A2 expression annotations in zebrafish. |
90 | Ortholog tissue expression 3 | Expression Databases | For the human gene HOXA1, which developmental stage has the most ortholog expression annotations in fly? | The embryo stage has the most HOXA1 expression annotations in fly. |
91 | PubMed search by variant name 1 | Literature | Search PubMed for articles about the specific mutation chr4:6302385 G>A. How many articles are there? Give the PMID for the top article. | One article found chr4:6302385 G>A, with PMID 38470317. |
92 | PubMed search by variant name 2 | Literature | Search PubMed Central (PMC) full-text articles for mentions of the gene PYROXD1 and the protein variant p.N155S in the same article. Try using all possible HGVS notations at different levels (protein change, coding DNA, and locus) to maximize search coverage. Return at least 3 but no more than 5 PMC IDs (PMCID). | Between 3 and 5 PMCIDs are returned for articles mentioning both PYROXD1 and p.N155S or its equivalent notations. |
93 | PubMed search by variant name 3 | Literature | Search PubMed for articles about the specific mutation NM_153682.3:c.2 T>C. How many articles are there? | One article about the mutation NM_153682.3:c.2 T > C is found. |
94 | STRING interaction counts 1 | Protein Interactions | How many protein interactions does NUTM2G have on STRING? | NUTM2G has 1 protein interaction on STRING. |
95 | STRING interaction counts 2 | Protein Interactions | How many protein interactions does PTPN11 have on STRING? | PTPN11 has 97 protein interactions on STRING. |
96 | STRING interaction counts 3 | Protein Interactions | How many protein interactions does TTN have on STRING? | TTN has 97 protein interactions on STRING. |
97 | STRING indirect connection 1 | Protein Interactions | Are there any proteins connected to both NUTM2G and VIRMA on STRING? Exclude NUTM2G and VIRMA themselves. If so, what proteins? | NUTM2G is directly connected to VIRMA but the two have no other shared protein connections on STRING. |
98 | STRING indirect connection 2 | Protein Interactions | Are there any proteins connected to both RASGRP1 and HRAS on STRING? Exclude RASGRP1 and HRAS themselves. If so, what proteins? | Yes, RASGRP1 is connected to HRAS through DGKZ. |
99 | STRING indirect connection 3 | Protein Interactions | Are there any proteins connected to both TTN and HBA1 on STRING? Exclude TTN and HBA1 themselves. If so, what proteins? | No, there are no proteins that are directly connected to both TTN and HBA1 on STRING. |
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