17-43808994-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001932.6(MPP3):c.1543C>T(p.Pro515Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001932.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MPP3 | NM_001932.6 | c.1543C>T | p.Pro515Ser | missense_variant | 19/20 | ENST00000398389.9 | NP_001923.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MPP3 | ENST00000398389.9 | c.1543C>T | p.Pro515Ser | missense_variant | 19/20 | 1 | NM_001932.6 | ENSP00000381425 | P1 | |
MPP3 | ENST00000398393.5 | c.1618C>T | p.Pro540Ser | missense_variant | 17/18 | 1 | ENSP00000381430 | |||
MPP3 | ENST00000496503.5 | c.*574C>T | 3_prime_UTR_variant, NMD_transcript_variant | 18/19 | 1 | ENSP00000465486 | ||||
MPP3 | ENST00000486600.1 | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2021 | The c.1543C>T (p.P515S) alteration is located in exon 19 (coding exon 17) of the MPP3 gene. This alteration results from a C to T substitution at nucleotide position 1543, causing the proline (P) at amino acid position 515 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
Publications
No publications associated with this variant yet.