Practical - Personnal genomics, variants

Structural variant

Go to dbVar (Database of Genomic Structural Variation) at NCBI.

Search the human TRPM1 gene, for that use the dbVar Advanced Search Builder.

Exercise 1 How many genomic variations listed in dbVar involve TRPM1 (in human)? What type of variants is the most represented? How many variants are pathogenic?

Search the nsv3924913 variant.

Exercise 2 What is the size of the region involved in the variation?

Exercise 3 Can we specifically assign these phenotypes to the TRPM1 gene? (in other words, this variant impact the TRPM1 gene?)

Exercise 4 On how many variant calls is this structural variant based?

Exercise 5 According to Genome view, is it the only structural variant in this genomic region? Display other studies using Genome view.

Exercise 6 Return to nsv3924913. What is the type (s) of variation for this variant?

Exercise 7 Display “clinical assertions”. What are the 3 links to ClinVar? What are the clinical features observed in patient with this variation associated with the loss a copy ? For that open the link begining with VCV00…

Exercise 8 On HPO. Search phenotypes associated with the loss of copy. Is the “Seizures” phenotype specific to a single disease?

Small variants

Go to dbSNP (Database of Short Genetic Variations) at NCBI.

Search the human TRPM1 gene, for that use the dbVar Advanced Search Builder.

Exercise 9 How many entries from the SNP database are linked to the TRPM1 gene?

Exercise 10 Among them, how many are pathogenic or likely pathogenic?

Exercise 11 What are their functional consequences? Why are some variants associated to several functional consequences?

Display the entry rs191205969

Exercise 12 What type of variant is it?

Exercise 13 What is the reference allele and the alternative one?

Exercise 14 What is the variant MAF in the 1000 genomes project? Can we speak of polymorphism?

Exercise 15 What is the meaning of NM_001252020.1: c.413T>C?

Exercise 16 What is the functional consequence of this variant? Is it associated with type 1C CSNB? - Is this variant present in all tested populations?

Display the entry rs267607140

Exercise 17 There are several functional consequences for this variant. Why?

Ensembl

In the Ensembl genome browser, display the TRPM1 gene and configure the page to display small variants from the 1000 genomes project and phenotypes associated.

For that, open the Configure Page windows. - Open Variation: activate 1000 Genomes - All - short variants (SNPs and indels) and 1000 Genomes - All - common - short variants (SNPs and indels) (with Normal style). - Open Variation > Phenotype, disease and curated variants_: activate All phenotype-associated - short variants (SNPs and indels) (with Normal style).

Exercise 18 What can you say about the distribution of these variants?

Exercise 19 What can you say about the location of variants associated to a phenotype?

Exercise 20 What other phenotypes and diseases are associated to TRPM1 variants in human?

Analysis of mutations

The TRPM1 gene of patients with CSNB (and in some cases their families) has been sequenced to find causative mutations for this rare disease.

Exercise 21 Several mutations identified in patients were considered non-pathogenic (see table below). Using this table and the ClinVar (NCBI), explain why these mutations are not pathogenic.

Exon	Nucleotide exchange	Allele state	Protein effect	SNP ID	Control Alleles (Mut/WT)
1	c.16C>T	het or hom	p.Arg6Trp	New	8/350 (T occurs also in Patypus)
11	c.1305G>A		p.Thr435Thr	rs1035705
3	c.161G>A		p.Ser54Asn	rs2241493
27	c.4123G>T	het	p.Glu1375X	New	20/320

Exercise 22 Mutations provided on Moodle were found in 3 patients and were considered as pathogenic. In each case, explain: why do they seem pathogenic, and the mode of transmission causing the disease.