Extract info on OMIM Phenotype

Question

[NB]

Hello,

I have around 900 gene symbols and its Gene ID (HGNC) for which I need to extract all its corresponding OMIM phenotype. Is there a way to do it or a tool that does this ?

For example, ABCA1 with HGNC ID 13666, the info to extract is listed here in column "Phenotype"

Thank you,

Answer 1

[finswimmer]

I guess quering OMIM itself isn't possible. But you can use BioMart for it:

• Database: Ensembl Genes
• Dataset: Human Genes
• Copy&Paste your gene names to: Filters --> Gene --> Input external references ID list --> Gene Name(s)
• Select Attributes --> Gene --> Gene name and Phenotype --> Phenotype description and Phenotype --> Source name
• Click Results

You can export the result as CSV or XLS. You can then filter the result for "MIM Morbid" in the "Source Name" column to get these phenotype reported by OMIM.

fin swimmer

[NB]

thank you so much! This works perfect!

Answer 2

[GenoMax]

Using EntrezDirect :

$ esearch -db omim -query "ABCA1" | esummary | xtract -pattern DocumentSummary -element Oid,Title
*613574 TETRATRICOPEPTIDE REPEAT DOMAIN-CONTAINING PROTEIN 39B; TTC39B
*613486 MICRO RNA 33B; MIR33B
*613004 HUNTINGTIN; HTT
*612156 MICRO RNA 33A; MIR33A

(info truncated for brevity)

or using medgen database

$ esearch -db medgen -query "ABCA1" | esummary | xtract -pattern DocumentSummary -element Title
ABCA1-Related Disorders
Caused by mutation in the ATP-binding cassette, subfamily A, member 1 gene (ABCA1, 600046.0001)
Familial hypoalphalipoproteinemia
Tangier disease
Familial hypertriglyceridemia
Familial hypercholesterolemia