2-144517279-GT-GTT
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_014795.4(ZEB2):c.71dupA(p.Asn24LysfsTer6) variant causes a frameshift, splice region change. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_014795.4 frameshift, splice_region
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZEB2 | NM_014795.4 | c.71dupA | p.Asn24LysfsTer6 | frameshift_variant, splice_region_variant | Exon 2 of 10 | ENST00000627532.3 | NP_055610.1 | |
ZEB2 | NM_001171653.2 | c.71dupA | p.Asn24LysfsTer6 | frameshift_variant, splice_region_variant | Exon 2 of 9 | NP_001165124.1 | ||
ZEB2 | NR_033258.2 | n.321dupA | splice_region_variant, non_coding_transcript_exon_variant | Exon 2 of 3 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Mowat-Wilson syndrome Pathogenic:2
For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 559637). This sequence change creates a premature translational stop signal (p.Asn24Lysfs*6) in the ZEB2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ZEB2 are known to be pathogenic (PMID: 16053902). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with ZEB2-related conditions. -
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at