rs1302511480
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_020998.4(MST1):āc.1754T>Cā(p.Leu585Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,130 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_020998.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250294Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135388
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461130Hom.: 0 Cov.: 40 AF XY: 0.00 AC XY: 0AN XY: 726880
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1754T>C (p.L585P) alteration is located in exon 15 (coding exon 15) of the MST1 gene. This alteration results from a T to C substitution at nucleotide position 1754, causing the leucine (L) at amino acid position 585 to be replaced by a proline (P). 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