X-154420709-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM1BS2
The NM_000116.5(TAFAZZIN):c.751C>T(p.Arg251Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000405 in 1,209,050 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 21 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_000116.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TAFAZZIN | NM_000116.5 | c.751C>T | p.Arg251Trp | missense_variant | Exon 10 of 11 | ENST00000601016.6 | NP_000107.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000541 AC: 6AN: 110874Hom.: 0 Cov.: 23 AF XY: 0.0000605 AC XY: 2AN XY: 33072
GnomAD3 exomes AF: 0.0000273 AC: 5AN: 183450Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67894
GnomAD4 exome AF: 0.0000392 AC: 43AN: 1098176Hom.: 0 Cov.: 31 AF XY: 0.0000523 AC XY: 19AN XY: 363534
GnomAD4 genome AF: 0.0000541 AC: 6AN: 110874Hom.: 0 Cov.: 23 AF XY: 0.0000605 AC XY: 2AN XY: 33072
ClinVar
Submissions by phenotype
not specified Uncertain:1
The p.Arg251Trp variant in TAZ has not been previously reported in individuals w ith cardiomyopathy, but has been identified in 2/47966 European chromosomes by t he Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs3 72689133). Computational prediction tools and conservation analysis do not provi de strong support for or against an impact to the protein. In summary, the clini cal significance of the p.Arg251Trp variant is uncertain. -
3-Methylglutaconic aciduria type 2 Uncertain:1
This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 251 of the TAZ protein (p.Arg251Trp). This variant is present in population databases (rs372689133, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with TAZ-related conditions. ClinVar contains an entry for this variant (Variation ID: 202095). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
not provided Uncertain:1
p.Arg251Trp (CGG>TGG): c.751 C>T in exon 10 of the TAZ gene (NM_000116.3). A variant of unknown significance has been identified in the TAZ gene. The R251W variant has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. The R251W variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The R251W variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved in mammals. In silico analysis predicts this variant likely does not alter the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic mutation or a rare benign variant. The variant is found in MITONUC-MITOP panel(s). -
Cardiovascular phenotype Uncertain:1
The p.R251W variant (also known as c.751C>T), located in coding exon 10 of the TAZ gene, results from a C to T substitution at nucleotide position 751. The arginine at codon 251 is replaced by tryptophan, an amino acid with dissimilar properties. Based on data from gnomAD, the T allele has an overall frequency of 0.0034% (7/204723) total alleles studied, with 2 hemizygote(s) observed. The highest observed frequency was 0.0065% (6/92362) of European (non-Finnish) alleles. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on the available evidence, the clinical significance of this variant remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at