2-238848570-C-T
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PP5_Moderate
The NM_001271893.4(TWIST2):c.355C>T(p.Gln119*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000569 in 1,582,640 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001271893.4 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TWIST2 | NM_001271893.4 | c.355C>T | p.Gln119* | stop_gained | Exon 1 of 2 | ENST00000612363.2 | NP_001258822.1 | |
TWIST2 | NM_057179.3 | c.355C>T | p.Gln119* | stop_gained | Exon 1 of 2 | NP_476527.1 | ||
TWIST2 | XR_007069137.1 | n.486C>T | non_coding_transcript_exon_variant | Exon 1 of 2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TWIST2 | ENST00000612363.2 | c.355C>T | p.Gln119* | stop_gained | Exon 1 of 2 | 1 | NM_001271893.4 | ENSP00000482581.1 | ||
TWIST2 | ENST00000448943.2 | c.355C>T | p.Gln119* | stop_gained | Exon 1 of 2 | 1 | ENSP00000405176.2 | |||
TWIST2 | ENST00000710607.1 | c.355C>T | p.Gln119* | stop_gained | Exon 1 of 2 | ENSP00000518373.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000996 AC: 2AN: 200756Hom.: 0 AF XY: 0.00000926 AC XY: 1AN XY: 107968
GnomAD4 exome AF: 0.00000419 AC: 6AN: 1430430Hom.: 0 Cov.: 31 AF XY: 0.00000282 AC XY: 2AN XY: 709084
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74364
ClinVar
Submissions by phenotype
Focal facial dermal dysplasia type III Pathogenic:1
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not provided Pathogenic:1
Published functional studies demonstrate that Q119X has a reduced ability to act as a transcription factor (Franco et al., 2011).; Nonsense variant in the C-terminus predicted to result in protein truncation, as the last 42 amino acids are lost; This variant is associated with the following publications: (PMID: 21801849, 20437613, 14069095, 20691403) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at