rs199712527
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_031310.3(PLVAP):c.988C>T(p.Gln330Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,312 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 Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. Q330Q) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_031310.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PLVAP | NM_031310.3 | c.988C>T | p.Gln330Ter | stop_gained | 3/6 | ENST00000252590.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PLVAP | ENST00000252590.9 | c.988C>T | p.Gln330Ter | stop_gained | 3/6 | 1 | NM_031310.3 | P1 | |
PLVAP | ENST00000595816.1 | c.79+496C>T | intron_variant | 3 | |||||
PLVAP | ENST00000599426.1 | c.517-12C>T | splice_polypyrimidine_tract_variant, intron_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460312Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 726570
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Diarrhea 10, protein-losing enteropathy type Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 20, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at