ClinVar Miner

Submissions for variant NM_000129.4(F13A1):c.1184C>T (p.Ala395Val)

gnomAD frequency: 0.00008  dbSNP: rs76451285
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001164367 SCV001326490 likely benign Factor XIII, A subunit, deficiency of 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Mendelics RCV002249746 SCV002519644 uncertain significance Thrombophilia due to thrombin defect 2023-01-25 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003323801 SCV004030018 benign not specified 2023-07-12 criteria provided, single submitter clinical testing Variant summary: F13A1 c.1184C>T (p.Ala395Val) results in a non-conservative amino acid change located in the transglutaminase-like domain (IPR002931) of the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00054 in 251472 control chromosomes, predominantly at a frequency of 0.0071 within the East Asian subpopulation in the gnomAD database, including 2 homozygotes. In addition, the variant was reported in the Japanese with an allele frequency of 0.059, i.e. in 6,385 / 108,604 alleles, including 198 homozygotes (in the jMorp database; PMID: 33179747), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.1184C>T in individuals affected with Factor XIIIA Deficiency and no experimental evidence demonstrating its impact on protein function have been reported. Two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. One submitter classified the variant as likely benign, and one submitter classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as benign.

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