20-4699336-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP3BP6
The NM_000311.5(PRNP):c.116C>T(p.Pro39Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000155 in 1,613,602 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P39P) has been classified as Likely benign.
Frequency
Consequence
NM_000311.5 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 | UniProt |
---|---|---|---|---|---|---|---|
PRNP | NM_000311.5 | c.116C>T | p.Pro39Leu | missense_variant | 2/2 | ENST00000379440.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRNP | ENST00000379440.9 | c.116C>T | p.Pro39Leu | missense_variant | 2/2 | 1 | NM_000311.5 | P1 | |
PRNP | ENST00000424424.2 | c.116C>T | p.Pro39Leu | missense_variant | 2/2 | 1 | P1 | ||
PRNP | ENST00000430350.2 | c.116C>T | p.Pro39Leu | missense_variant | 2/2 | 1 | P1 | ||
PRNP | ENST00000457586.2 | c.116C>T | p.Pro39Leu | missense_variant | 2/2 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000659 AC: 1AN: 151800Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000361 AC: 9AN: 249140Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135394
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461802Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727206
GnomAD4 genome ? AF: 0.00000659 AC: 1AN: 151800Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74108
ClinVar
Submissions by phenotype
Huntington disease-like 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Mar 03, 2020 | This variant has been observed in individual(s) with frontotemporal dementia (PMID: 25022973, 26757195). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C65"). This variant is present in population databases (rs747019990, ExAC 0.006%). This sequence change replaces proline with leucine at codon 39 of the PRNP protein (p.Pro39Leu). The proline residue is highly conserved and there is a moderate physicochemical difference between proline and leucine. - |
Inherited prion disease Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Oct 16, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at