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GALT

From SNPedia

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# SNPs221
 Max MagnitudeChromosome positionSummary
rs111033634034,646,745
rs111033635034,646,771
rs111033636034,646,786
rs111033637034,646,731
rs111033638034,646,722
rs111033639034,646,705
rs111033640334,646,586
rs111033643034,647,097
rs111033644034,647,101
rs111033645034,647,113
rs111033646034,647,119
rs111033647034,647,136
rs111033648034,647,158
rs111033649034,647,166
rs111033651034,647,140
rs111033652034,647,140
rs111033654034,647,169
rs111033655034,647,213
rs111033656034,647,203
rs111033658034,647,205
rs111033659034,647,226
rs111033660034,647,253
rs111033661034,647,490
rs111033662034,647,226
rs111033663034,647,227
rs111033664034,647,244
rs111033665034,647,247
rs111033666034,647,504
rs111033667034,647,655
rs111033668034,647,524
rs111033669034,647,529
rs111033670034,647,531
rs111033673034,647,682
rs111033674034,647,695
rs111033675034,647,696
rs111033676034,647,661
rs111033677034,647,665
rs111033678034,647,669
rs111033679034,647,678
rs111033680034,647,702
rs111033681034,647,706
rs111033682034,647,833
rs111033683034,647,840
rs111033684034,647,846
rs111033686034,647,867
rs111033687034,647,870
rs111033688034,647,848
rs111033689034,647,854
rs111033690034,647,858
rs111033692034,647,878
... further results


A fairly well known deletion potentially resulting in galactosemia consists of a ~5kb+ chunk out of the GALT gene on ch 9, predominantly seen in Ashkenazi Jews.[PMID 17079880] Seen in perhaps up to 10% of carriers, it does wipe out several SNPs so it should be possible to predict a deletion based on seeing either (a) a significant run of "absent" calls for chromosomally adjacent SNPs, assuming homozygosity for deleted areas on both maternal and paternal chromosomes, or (b) seeing a statistically unlikely run of homozygosity for a string of chromosomally adjacent SNPs on an autosome, assuming the deletion is only occurring on one chromosome.

Technically, the 5kb deletion allele is complex, in that it involves a 3163-nt deletion of the GALT promoter and 5' gene region along with a 2295-bp deletion of a portion of towards the 3' end of the gene; only segments of exon 8 and intron 8 are retained [PMID 17079880].