ClinVar Miner

Submissions for variant NM_001377265.1(MAPT):c.896T>G (p.Val299Gly)

gnomAD frequency: 0.00235  dbSNP: rs141120474
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000761992 SCV000892222 uncertain significance not provided 2021-12-01 criteria provided, single submitter clinical testing
Invitae RCV001510129 SCV001717078 benign Frontotemporal dementia 2021-01-29 criteria provided, single submitter clinical testing
GeneDx RCV000761992 SCV001858921 benign not provided 2019-08-05 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 22906081, 23990795, 25617006, 29525178, 25104557, 25937274)
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000761992 SCV001553334 likely benign not provided no assertion criteria provided clinical testing The MAPT p.Val224Gly variant was identified in 2 of 282 proband chromosomes (frequency: 0.007) from individuals with late onset Alzheimer's and was present in 1 of 358 control chromosomes (frequency: 0.003) from healthy individuals (Sassi_2014_PMID:25104557). Another study identified the p.V224G variant in 3 of 460 control individuals but not in 517 Parkinson's patients (Iqbal_2016_PMID:27329738). The variant was identified in dbSNP (ID: rs141120474), Cosmic, ClinVar (classified as uncertain significance by CeGaT Praxis fuer Humangenetik Tuebingen) and LOVD 3.0 (classified as likely benign three times and a VUS). The variant was also identified in control databases in 587 of 275134 chromosomes (1 homozygous) at a frequency of 0.002134 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (non-Finnish) in 450 of 123792 chromosomes (freq: 0.003635), Other in 19 of 7058 chromosomes (freq: 0.002692), Ashkenazi Jewish in 25 of 10060 chromosomes (freq: 0.002485), Latino in 59 of 35178 chromosomes (freq: 0.001677), African in 21 of 24144 chromosomes (freq: 0.00087), European (Finnish) in 12 of 24802 chromosomes (freq: 0.000484) and South Asian in 1 of 30292 chromosomes (freq: 0.000033), but was not observed in the East Asian population. The p.Val224 residue is not conserved in mammals and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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