rs1131692164
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_020699.4(GATAD2B):c.80_81insGATGT(p.Leu28MetfsTer18) variant causes a frameshift change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
GATAD2B
NM_020699.4 frameshift
NM_020699.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.98
Genes affected
GATAD2B (HGNC:30778): (GATA zinc finger domain containing 2B) This gene encodes a zinc finger protein transcriptional repressor. The encoded protein is part of the methyl-CpG-binding protein-1 complex, which represses gene expression by deacetylating methylated nucleosomes. Mutations in this gene are linked to intellectual disability and dysmorphic features associated with cognitive disability. [provided by RefSeq, Jun 2016]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. There are 64 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 1-153828267-G-GACATC is Pathogenic according to our data. Variant chr1-153828267-G-GACATC is described in ClinVar as [Pathogenic]. Clinvar id is 430624.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GATAD2B | NM_020699.4 | c.80_81insGATGT | p.Leu28MetfsTer18 | frameshift_variant | 2/11 | ENST00000368655.5 | |
GATAD2B | XM_047426115.1 | c.83_84insGATGT | p.Leu29MetfsTer18 | frameshift_variant | 2/11 | ||
GATAD2B | XM_047426117.1 | c.80_81insGATGT | p.Leu28MetfsTer18 | frameshift_variant | 2/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GATAD2B | ENST00000368655.5 | c.80_81insGATGT | p.Leu28MetfsTer18 | frameshift_variant | 2/11 | 1 | NM_020699.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 22, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at