chr9-101286224-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_207299.2(PLPPR1):āc.373A>Gā(p.Ile125Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,613,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_207299.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLPPR1 | NM_207299.2 | c.373A>G | p.Ile125Val | missense_variant | 4/8 | ENST00000374874.8 | |
PLPPR1 | NM_017753.3 | c.373A>G | p.Ile125Val | missense_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLPPR1 | ENST00000374874.8 | c.373A>G | p.Ile125Val | missense_variant | 4/8 | 1 | NM_207299.2 | P1 | |
PLPPR1 | ENST00000395056.2 | c.373A>G | p.Ile125Val | missense_variant | 4/8 | 1 | P1 | ||
PLPPR1 | ENST00000463206.1 | n.388A>G | non_coding_transcript_exon_variant | 2/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152244Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251164Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135744
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461524Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727054
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2023 | The c.373A>G (p.I125V) alteration is located in exon 4 (coding exon 3) of the PLPPR1 gene. This alteration results from a A to G substitution at nucleotide position 373, causing the isoleucine (I) at amino acid position 125 to be replaced by a valine (V). 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