ClinVar Miner

Submissions for variant NM_002299.4(LCT):c.4170T>A (p.Tyr1390Ter) (rs121908936)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
OMIM RCV000006964 SCV000027160 pathogenic Congenital lactase deficiency 2006-02-01 no assertion criteria provided literature only
Reproductive Health Research and Development,BGI Genomics RCV000006964 SCV001142323 pathogenic Congenital lactase deficiency 2020-01-06 no assertion criteria provided curation NM_002299.2:c.4170T>A in the LCT gene has an allele frequency of 0.01 in European (Finnish) subpopulation in the gnomAD database. Twenty-seven patients out of 32 (84%) affected with congenital lactase deficiency were homozygous for this nonsense mutation, c.4170T>A (p.Y1390X) (PMID: 16400612). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. Taken together, we interprete this variant as Pathogenic/Likely pathogenic. ACMG/AMP Criteria applied: PVS1; PS4.

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