16-1724639-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001318852.2(MAPK8IP3):c.401G>A(p.Arg134His) variant causes a missense change. The variant allele was found at a frequency of 0.0000031 in 1,613,438 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001318852.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAPK8IP3 | NM_001318852.2 | c.401G>A | p.Arg134His | missense_variant | Exon 2 of 32 | ENST00000610761.2 | NP_001305781.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAPK8IP3 | ENST00000610761.2 | c.401G>A | p.Arg134His | missense_variant | Exon 2 of 32 | 1 | NM_001318852.2 | ENSP00000481780.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152254Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000804 AC: 2AN: 248824Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135228
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461184Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 726878
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74386
ClinVar
Submissions by phenotype
Neurodevelopmental disorder with or without variable brain abnormalities; NEDBA Uncertain:1
The missense variant c.401G>A (p.Arg134His) in MAPK8IP3 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Arg134His variant is reported with allele frequency 0.0008% in gnomAD exomes and novel in 1000 Genomes. The amino acid Arg at position 134 is changed to a His changing protein sequence and it might alter its composition and physico-chemical properties. The amino acid change p.Arg134His in MAPK8IP3 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance . -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at