19-4345820-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001300862.2(MPND):c.370C>T(p.Pro124Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000669 in 1,613,862 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001300862.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MPND | NM_001300862.2 | c.370C>T | p.Pro124Ser | missense_variant | Exon 3 of 13 | ENST00000599840.6 | NP_001287791.1 | |
MPND | NM_032868.6 | c.370C>T | p.Pro124Ser | missense_variant | Exon 3 of 12 | NP_116257.2 | ||
MPND | NM_001159846.3 | c.370C>T | p.Pro124Ser | missense_variant | Exon 3 of 11 | NP_001153318.1 | ||
MPND | XM_006722926.3 | c.370C>T | p.Pro124Ser | missense_variant | Exon 3 of 13 | XP_006722989.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000843 AC: 21AN: 249092Hom.: 0 AF XY: 0.000140 AC XY: 19AN XY: 135274
GnomAD4 exome AF: 0.0000698 AC: 102AN: 1461680Hom.: 1 Cov.: 32 AF XY: 0.0000798 AC XY: 58AN XY: 727148
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.370C>T (p.P124S) alteration is located in exon 3 (coding exon 3) of the MPND gene. This alteration results from a C to T substitution at nucleotide position 370, causing the proline (P) at amino acid position 124 to be replaced by a serine (S). 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