rs777250096
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP2PP3
The NM_005120.3(MED12):c.4021C>T(p.Arg1341Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000199 in 1,207,320 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 7 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1341Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_005120.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MED12 | NM_005120.3 | c.4021C>T | p.Arg1341Trp | missense_variant | 28/45 | ENST00000374080.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MED12 | ENST00000374080.8 | c.4021C>T | p.Arg1341Trp | missense_variant | 28/45 | 1 | NM_005120.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000177 AC: 2AN: 113207Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 35343
GnomAD3 exomes AF: 0.00000575 AC: 1AN: 173825Hom.: 0 AF XY: 0.0000166 AC XY: 1AN XY: 60421
GnomAD4 exome AF: 0.0000201 AC: 22AN: 1094113Hom.: 0 Cov.: 33 AF XY: 0.0000194 AC XY: 7AN XY: 359991
GnomAD4 genome ? AF: 0.0000177 AC: 2AN: 113207Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 35343
ClinVar
Submissions by phenotype
X-linked intellectual disability with marfanoid habitus Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory of Medical Genetics, National & Kapodistrian University of Athens | Jul 05, 2018 | PP2, PP3 - |
Familial thoracic aortic aneurysm and aortic dissection Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 20, 2021 | The p.R1341W variant (also known as c.4021C>T), located in coding exon 28 of the MED12 gene, results from a C to T substitution at nucleotide position 4021. The arginine at codon 1341 is replaced by tryptophan, an amino acid with dissimilar properties. Based on data from gnomAD, the T allele has an overall frequency of 0.0005753% (1/173825) total alleles studied, with 1 hemizygote(s) observed. The highest observed frequency was 0.001293% (1/77358) of European (non-Finnish) alleles. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Nov 28, 2017 | The R1341W variant of uncertain significance in the MED12 gene has not been published as a pathogenic or benign variant to our knowledge. This variant has been identified independently of additional cardiogenetic variants in one other individual referred for Marfan/TAAD genetic testing at GeneDx; however, thus far, segregation data is absent for these individuals due to the lack of clinical information provided and insufficient participation by informative family members. The R1341W variant was not observed in approximately 6,100 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 R1341W 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 also occurs at a position that is conserved across species. Consequently, in silico analysis predicts this variant is probably damaging to the protein structure/function. Nevertheless, no missense variants in nearby residues have been reported in the Human Gene Mutation Database in association with MED12-related disorders (Stenson et al., 2014). Therefore, based on the currently available information, it is unclear whether this variant is pathogenic or rare benign. - |
FG syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 11, 2024 | This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 1341 of the MED12 protein (p.Arg1341Trp). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with clinical features of MED12-related conditions (PMID: 34008892). ClinVar contains an entry for this variant (Variation ID: 213641). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt MED12 protein function with a positive predictive value of 95%. 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at