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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

Genomes: not found (cov: 34)

Consequence

MLC1
NM_015166.4 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: 2.94
Variant links:
Genes affected
MLC1 (HGNC:17082): (modulator of VRAC current 1) The function of this gene product is unknown; however, homology to other proteins suggests that it may be an integral membrane transporter. Mutations in this gene have been associated with megalencephalic leukoencephalopathy with subcortical cysts, an autosomal recessive neurological disorder. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in NM_015166.4

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MLC1NM_015166.4 linkc.921_929dupGCTGCTGCT p.Leu308_Leu310dup disruptive_inframe_insertion Exon 11 of 12 ENST00000311597.10 NP_055981.1 Q15049-1A0A024R4V4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MLC1ENST00000311597.10 linkc.921_929dupGCTGCTGCT p.Leu308_Leu310dup disruptive_inframe_insertion Exon 11 of 12 1 NM_015166.4 ENSP00000310375.6 Q15049-1
MLC1ENST00000395876.6 linkc.921_929dupGCTGCTGCT p.Leu308_Leu310dup disruptive_inframe_insertion Exon 11 of 12 1 ENSP00000379216.2 Q15049-1
MLC1ENST00000483836.1 linkn.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

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Megalencephalic leukoencephalopathy with subcortical cysts 1 Uncertain:1
Apr 24, 2017
Counsyl
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not provided Uncertain:1
Feb 10, 2022
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs761096481; hg19: chr22-50502592; API