ClinVar Miner

Submissions for variant NM_004615.3(TSPAN7):c.515C>A (p.Pro172His) (rs104894951)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000721059 SCV000851944 uncertain significance History of neurodevelopmental disorder 2012-10-12 criteria provided, single submitter clinical testing In published studies involving a family with six affected males with non-syndromic X-linked mental retardation, this variant was present in all individuals with mental retardation and in one male whose IQ score is within the normal range (Zemni R et al. Nat Genet. 2000;24(2):167-170 and Gomot M et al. Am J Med Genet. 2002;112:400-404). In a separate study, this variant was observed in 1/105 males with mental retardation, and it was absent in this particular proband's unaffected brother (Maranduba CM et al. Am J Med Genet. 2004;124A:413-415). This variant has not been detected in conjunction with a pathogenic mutation to date.Based on data from the NHLBI Exome Sequencing Project (ESP), the A-allele has an overall frequency of approximately 0.05% (1/1997) in male alleles studied. The A-allele was observed in 0.07% (1/1475) of European American male alleles but was absent in 522 African American male alleles and was not observed in the homozygous state in 3381 female alleles studied (http://snp.gs.washington.edu/EVS). Furthermore, this variant was not detected in a total of 420 normal X chromosomes in all of the published studies. This amino acid position is not conserved on species alignment.This alteration is predicted to be benign with a score of 0.327 (sensitivity: 0.86; specificity: 0.76)This alteration is predicted to be tolerated with a score of 0.190 (conservation: 1.91)
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne RCV000012396 SCV000883120 likely benign Mental retardation 58, X-linked 2018-11-21 criteria provided, single submitter clinical testing
Invitae RCV000904077 SCV001048575 likely benign not provided 2018-12-21 criteria provided, single submitter clinical testing
Mendelics RCV000012396 SCV001141830 uncertain significance Mental retardation 58, X-linked 2019-05-28 criteria provided, single submitter clinical testing
OMIM RCV000012396 SCV000032630 pathogenic Mental retardation 58, X-linked 2004-02-01 no assertion criteria provided literature only

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