19-35718020-T-TGGCGGCGGCGGCG
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_014727.3(KMT2B):c.12_24dup(p.Ser9_?8) variant causes a frameshift, start lost change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Genomes: not found (cov: 32)
Consequence
KMT2B
NM_014727.3 frameshift, start_lost
NM_014727.3 frameshift, start_lost
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.788
Genes affected
KMT2B (HGNC:15840): (lysine methyltransferase 2B) This gene encodes a protein which contains multiple domains including a CXXC zinc finger, three PHD zinc fingers, two FY-rich domains, and a SET (suppressor of variegation, enhancer of zeste, and trithorax) domain. The SET domain is a conserved C-terminal domain that characterizes proteins of the MLL (mixed-lineage leukemia) family. This gene is ubiquitously expressed in adult tissues. It is also amplified in solid tumor cell lines, and may be involved in human cancer. Two alternatively spliced transcript variants encoding distinct isoforms have been reported for this gene, however, the full length nature of the shorter transcript is not known. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 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 95 pathogenic variants in the truncated region.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 19-35718020-T-TGGCGGCGGCGGCG is Pathogenic according to our data. Variant chr19-35718020-T-TGGCGGCGGCGGCG is described in ClinVar as [Pathogenic]. Clinvar id is 450816.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KMT2B | NM_014727.3 | c.12_24dup | p.Ser9_?8 | frameshift_variant, start_lost | 1/37 | ENST00000420124.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KMT2B | ENST00000420124.4 | c.12_24dup | p.Ser9_?8 | frameshift_variant, start_lost | 1/37 | 1 | NM_014727.3 | P2 | |
KMT2B | ENST00000673918.2 | c.12_24dup | p.Ser9_?8 | frameshift_variant, start_lost | 1/37 | A2 | |||
KMT2B | ENST00000687718.1 | c.12_24dup | p.Ser9_?8 | frameshift_variant, start_lost, NMD_transcript_variant | 1/3 | ||||
KMT2B | ENST00000692961.1 | c.12_24dup | p.Ser9_?8 | frameshift_variant, start_lost, NMD_transcript_variant | 1/36 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Dec 01, 2021 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Mar 19, 2019 | Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 33150406) - |
Inborn genetic diseases Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 01, 2023 | The c.12_24dup13 (p.S9Gfs*111) alteration, located in exon 1 (coding exon 1) of the KMT2B gene, consists of a duplication of GGCGGGCGGCGGC at position 12, causing a translational frameshift with a predicted alternate stop codon after 111 amino acids. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This alteration was reported de novo in an individual with features consistent with KMT2B-related early-onset complex dystonia (Cif, 2020). Based on the available evidence, this alteration is classified as pathogenic. - |
Dystonia 28, childhood-onset Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Undiagnosed Diseases Network, NIH | Apr 18, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at