4-75860903-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 4P and 4B. PM1PP3_ModerateBS2
The NM_006239.3(PPEF2):c.2026G>A(p.Glu676Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000275 in 1,614,090 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006239.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPEF2 | ENST00000286719.12 | c.2026G>A | p.Glu676Lys | missense_variant | Exon 17 of 17 | 1 | NM_006239.3 | ENSP00000286719.6 | ||
PPEF2 | ENST00000511880.7 | n.*2431G>A | non_coding_transcript_exon_variant | Exon 18 of 18 | 1 | ENSP00000426186.2 | ||||
PPEF2 | ENST00000511880.7 | n.*2431G>A | 3_prime_UTR_variant | Exon 18 of 18 | 1 | ENSP00000426186.2 | ||||
PPEF2 | ENST00000652700.1 | c.535G>A | p.Glu179Lys | missense_variant | Exon 6 of 6 | ENSP00000498558.1 |
Frequencies
GnomAD3 genomes AF: 0.000204 AC: 31AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000184 AC: 46AN: 250642Hom.: 0 AF XY: 0.000214 AC XY: 29AN XY: 135536
GnomAD4 exome AF: 0.000283 AC: 413AN: 1461748Hom.: 2 Cov.: 31 AF XY: 0.000261 AC XY: 190AN XY: 727138
GnomAD4 genome AF: 0.000203 AC: 31AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74506
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2026G>A (p.E676K) alteration is located in exon 17 (coding exon 16) of the PPEF2 gene. This alteration results from a G to A substitution at nucleotide position 2026, causing the glutamic acid (E) at amino acid position 676 to be replaced by a lysine (K). 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