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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP3
The NM_015166.4(MLC1):c.921_929dupGCTGCTGCT(p.Leu308_Leu310dup) variant causes a disruptive inframe insertion 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 Uncertain significance (★★).
Frequency
Consequence
NM_015166.4 disruptive_inframe_insertion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MLC1 | NM_015166.4 | c.921_929dupGCTGCTGCT | p.Leu308_Leu310dup | disruptive_inframe_insertion | Exon 11 of 12 | ENST00000311597.10 | NP_055981.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MLC1 | ENST00000311597.10 | c.921_929dupGCTGCTGCT | p.Leu308_Leu310dup | disruptive_inframe_insertion | Exon 11 of 12 | 1 | NM_015166.4 | ENSP00000310375.6 | ||
MLC1 | ENST00000395876.6 | c.921_929dupGCTGCTGCT | p.Leu308_Leu310dup | disruptive_inframe_insertion | Exon 11 of 12 | 1 | ENSP00000379216.2 | |||
MLC1 | ENST00000483836.1 | n.278_286dupGCTGCTGCT | non_coding_transcript_exon_variant | Exon 4 of 5 | 2 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome Cov.: 39
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Megalencephalic leukoencephalopathy with subcortical cysts 1 Uncertain:1
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not provided Uncertain:1
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. This variant has not been reported in the literature in individuals affected with MLC1-related conditions. This variant is not present in population databases (gnomAD no frequency). This variant, c.921_929dup, results in the insertion of 3 amino acid(s) of the MLC1 protein (p.Leu308_Leu310dup), but otherwise preserves the integrity of the reading frame. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at