17-61950920-C-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_005121.3(MED13):c.6196G>T(p.Gly2066Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005121.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MED13 | NM_005121.3 | c.6196G>T | p.Gly2066Cys | missense_variant | Exon 28 of 30 | ENST00000397786.7 | NP_005112.2 | |
MED13 | XM_011525551.3 | c.6037G>T | p.Gly2013Cys | missense_variant | Exon 27 of 29 | XP_011523853.1 | ||
MED13 | XM_011525553.4 | c.5527G>T | p.Gly1843Cys | missense_variant | Exon 25 of 27 | XP_011523855.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.6196G>T (p.G2066C) alteration is located in exon 28 (coding exon 28) of the MED13 gene. This alteration results from a G to T substitution at nucleotide position 6196, causing the glycine (G) at amino acid position 2066 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at