NM_001146154.2:c.416C>A
Variant summary
Our verdict is Likely pathogenic. The variant received 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001146154.2(PTGR2):c.416C>A(p.Thr139Asn) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,602 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T139S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001146154.2 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_pathogenic. The variant received 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PTGR2 | ENST00000555661.6 | c.416C>A | p.Thr139Asn | missense_variant | Exon 5 of 10 | 1 | NM_001146154.2 | ENSP00000452280.1 | ||
ENSG00000258653 | ENST00000556551.2 | n.416C>A | non_coding_transcript_exon_variant | Exon 5 of 22 | 2 | ENSP00000451484.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461602Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727132 show subpopulations
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at