X-154779320-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_002436.4(MPP1):c.1258G>A(p.Glu420Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,208,875 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002436.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000178 AC: 2AN: 112201Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34347
GnomAD4 exome AF: 0.00000638 AC: 7AN: 1096674Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 4AN XY: 362072
GnomAD4 genome AF: 0.0000178 AC: 2AN: 112201Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34347
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1258G>A (p.E420K) alteration is located in exon 12 (coding exon 12) of the MPP1 gene. This alteration results from a G to A substitution at nucleotide position 1258, causing the glutamic acid (E) at amino acid position 420 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at