1-98956645-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001037317.2(PLPPR5):āc.334A>Gā(p.Ile112Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000483 in 1,449,592 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001037317.2 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 |
---|---|---|---|---|---|---|---|---|
PLPPR5 | NM_001037317.2 | c.334A>G | p.Ile112Val | missense_variant | 2/6 | ENST00000263177.5 | NP_001032394.1 | |
PLPPR5 | NM_001010861.3 | c.334A>G | p.Ile112Val | missense_variant | 2/6 | NP_001010861.1 | ||
PLPPR5 | XM_011540838.4 | c.286A>G | p.Ile96Val | missense_variant | 3/7 | XP_011539140.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLPPR5 | ENST00000263177.5 | c.334A>G | p.Ile112Val | missense_variant | 2/6 | 1 | NM_001037317.2 | ENSP00000263177 | P4 | |
PLPPR5 | ENST00000370188.7 | c.334A>G | p.Ile112Val | missense_variant | 2/6 | 1 | ENSP00000359207 | A1 | ||
PLPPR5 | ENST00000672681.1 | c.334A>G | p.Ile112Val | missense_variant | 2/7 | ENSP00000500930 | ||||
PLPPR5 | ENST00000696571.1 | c.169A>G | p.Ile57Val | missense_variant | 3/7 | ENSP00000512726 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000483 AC: 7AN: 1449592Hom.: 0 Cov.: 30 AF XY: 0.00000277 AC XY: 2AN XY: 720824
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2023 | The c.334A>G (p.I112V) alteration is located in exon 2 (coding exon 2) of the PLPPR5 gene. This alteration results from a A to G substitution at nucleotide position 334, causing the isoleucine (I) at amino acid position 112 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
Publications
No publications associated with this variant yet.