rs104894181
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_001083116.3(PRF1):c.1286G>A(p.Gly429Glu) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,528 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. G429G) has been classified as Likely benign.
Frequency
Consequence
NM_001083116.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRF1 | NM_001083116.3 | c.1286G>A | p.Gly429Glu | missense_variant | 3/3 | ENST00000441259.2 | |
PRF1 | NM_005041.6 | c.1286G>A | p.Gly429Glu | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRF1 | ENST00000441259.2 | c.1286G>A | p.Gly429Glu | missense_variant | 3/3 | 5 | NM_001083116.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249912Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135370
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461528Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727060
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Familial hemophagocytic lymphohistiocytosis 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Dec 03, 1999 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at