rs281875317
Variant summary
Our verdict is Pathogenic. Variant got 24 ACMG points: 24P and 0B. PS1_Very_StrongPM2PM5PP3_StrongPP5_Very_Strong
The NM_015166.4(MLC1):c.634G>C(p.Gly212Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G212E) has been classified as Likely pathogenic.
Frequency
Consequence
NM_015166.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 24 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MLC1 | NM_015166.4 | c.634G>C | p.Gly212Arg | missense_variant | 8/12 | ENST00000311597.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MLC1 | ENST00000311597.10 | c.634G>C | p.Gly212Arg | missense_variant | 8/12 | 1 | NM_015166.4 | P1 | |
MLC1 | ENST00000395876.6 | c.634G>C | p.Gly212Arg | missense_variant | 8/12 | 1 | P1 | ||
MLC1 | ENST00000442311.1 | c.544G>C | p.Gly182Arg | missense_variant | 7/8 | 5 | |||
MLC1 | ENST00000470008.1 | n.114G>C | non_coding_transcript_exon_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Megalencephalic leukoencephalopathy with subcortical cysts 1 Pathogenic:2
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Jan 30, 2023 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Aug 16, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at