14-55063128-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000395468.9(MAPK1IP1L):c.529C>T(p.Pro177Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,461,476 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000395468.9 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 |
---|---|---|---|---|---|---|---|---|
MAPK1IP1L | NM_144578.4 | c.529C>T | p.Pro177Ser | missense_variant | 3/4 | ENST00000395468.9 | NP_653179.1 | |
MAPK1IP1L | XM_011537362.3 | c.535C>T | p.Pro179Ser | missense_variant | 3/4 | XP_011535664.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAPK1IP1L | ENST00000395468.9 | c.529C>T | p.Pro177Ser | missense_variant | 3/4 | 1 | NM_144578.4 | ENSP00000378851.3 | ||
MAPK1IP1L | ENST00000553976.1 | n.178C>T | non_coding_transcript_exon_variant | 1/3 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251278Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135818
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461476Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727050
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.529C>T (p.P177S) alteration is located in exon 3 (coding exon 2) of the MAPK1IP1L gene. This alteration results from a C to T substitution at nucleotide position 529, causing the proline (P) at amino acid position 177 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