NM_001527.4:c.1318_1321delAAAG
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001527.4(HDAC2):c.1318_1321delAAAG(p.Lys440GlufsTer65) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001527.4 frameshift
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HDAC2 | NM_001527.4 | c.1318_1321delAAAG | p.Lys440GlufsTer65 | frameshift_variant | Exon 12 of 14 | ENST00000519065.6 | NP_001518.3 | |
HDAC2 | XM_047418692.1 | c.1228_1231delAAAG | p.Lys410GlufsTer65 | frameshift_variant | Exon 12 of 14 | XP_047274648.1 | ||
HDAC2 | NR_033441.2 | n.1586_1589delAAAG | non_coding_transcript_exon_variant | Exon 13 of 15 | ||||
HDAC2 | NR_073443.2 | n.1516_1519delAAAG | non_coding_transcript_exon_variant | Exon 12 of 14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HDAC2 | ENST00000519065.6 | c.1318_1321delAAAG | p.Lys440GlufsTer65 | frameshift_variant | Exon 12 of 14 | 1 | NM_001527.4 | ENSP00000430432.1 | ||
HDAC2 | ENST00000368632.6 | c.1228_1231delAAAG | p.Lys410GlufsTer65 | frameshift_variant | Exon 13 of 15 | 2 | ENSP00000357621.2 | |||
HDAC2 | ENST00000519108.5 | c.1228_1231delAAAG | p.Lys410GlufsTer65 | frameshift_variant | Exon 12 of 14 | 2 | ENSP00000430008.1 | |||
HDAC2 | ENST00000523334.1 | n.4321_4324delAAAG | non_coding_transcript_exon_variant | Exon 6 of 8 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
HDAC2-related disorder Uncertain:1
The HDAC2 c.1318_1321delAAAG variant is predicted to result in a frameshift and premature protein termination (p.Lys440Glufs*65). To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. Loss of function is not a conclusively established mechanism for HDAC2-related disease and only a few protein truncating variants have been reported to date (Kaplanis et al. 2020. PubMed ID: 33057194; Human Gene Mutation Database, http://www.hgmd.cf.ac.uk/ac/index.php). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.