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Day 9 - OMIM

posted Jul 11, 2011, 9:10 AM by Colm O'Dushlaine   [ updated Jul 11, 2011, 11:07 AM ]
Can we identify any SNPs, predicted to be damaging, in OMIM? This would point to any Mendelian traits/disorders I might have. There is a file in dbSNP that is useful for this - ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/organism_data/OmimVarLocusIdSNP.bcp.gz. The file links omim ids to SNP ids. 

In UNIX:

  wget ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/database/organism_data/OmimVarLocusIdSNP.bcp.gz
 gunzip OmimVarLocusIdSNP.bcp.gz
 cut -f 1,9 OmimVarLocusIdSNP.bcp | gawk '{print "rs"$2,$1 }' | sort > snps_2_omim.txt

Then, sort my missense SNPs and join both lists. None of my rare missense match, so I checked the larger list of all 476 missense SNPs:

 join all_missense.sorted.txt snps_2_omim.txt 

You can then just look up the OMIM entries listed, e.g. http://omim.org/entry/607751 

rs10246939 607751 <-- This polymorphism, in conjunction with other SNPs in the gene, give rise to the ability to taste or not taste phenylthiocarbamide
rs1049550 612388 <--  strongly associated with sarcoidosis
rs1051740 132810 <-- LYMPHOPROLIFERATIVE DISORDERS, SUSCEPTIBILITY TO
rs1126809 601800 <-- association with skin sensitivity to sun (p = 7.1 x 10(-13)) and blue versus green eye color (p = 4.6 x 10(-21)).
rs1126809 606933 <-- blue eye colour
rs1154510 609695 <-- HAWKINSINURIA (autosomal dominant inborn error of metabolism) (elevated levels of blood tyrosine and massive excretion of tyrosine derivatives into urine)
rs2108622 122700 <-- resistance to warfarin
rs2108622 604426 <-- resistance to warfarin
rs288326 605083 <-- OSTEOARTHRITIS SUSCEPTIBILITY 1 (strong risk factor for primary osteoarthritis of the hip in females)
rs3775291 603029 <-- protective against the development of geographic atrophy or advanced dry age-related macular degeneration
rs3775291 603075 <-- associated with protection from progression to geographic atrophy in patients with age-related macular degeneration
rs4673 608508 <-- cardiovascular disease related
rs4917 138680 <-- an increased risk for leanness (OR, 1.90; p = 0.027)
rs602662 182100 <-- ...genetic factors affecting circulating vitamin B12 levels and identified rs602662 in the FUT2 gene
rs602662 612542 <-- vit B12
rs61630004 602767 <-- ECTODERMAL DYSPLASIA, 'PURE' HAIR-NAIL TYPE
rs7080536 603924 <-- CAROTID STENOSIS, SUSCEPTIBILITY TO (basically a heart disease risk factor)
rs7133914 609007 <-- Decreased susceptibility to Parkinson Disease
rs7308720 609007 <-- Decreased susceptibility to Parkinson Disease

So, overall I think some interesting stuff in there, although alot of this is covered nicely by 23&me already.

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