10-120575181-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001030059.3(PLPP4):c.496C>T(p.His166Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,613,866 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001030059.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLPP4 | ENST00000398250.6 | c.496C>T | p.His166Tyr | missense_variant | Exon 6 of 7 | 1 | NM_001030059.3 | ENSP00000381302.1 | ||
PLPP4 | ENST00000369073.3 | n.466C>T | non_coding_transcript_exon_variant | Exon 6 of 7 | 5 | |||||
PLPP4 | ENST00000496437.1 | n.-7C>T | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249330Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135258
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461694Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 727158
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.496C>T (p.H166Y) alteration is located in exon 6 (coding exon 6) of the PLPP4 gene. This alteration results from a C to T substitution at nucleotide position 496, causing the histidine (H) at amino acid position 166 to be replaced by a tyrosine (Y). 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