rs776190040
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_022835.3(PLEKHG2):c.122C>T(p.Pro41Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000133 in 1,596,314 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_022835.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLEKHG2 | NM_022835.3 | c.122C>T | p.Pro41Leu | missense_variant | Exon 3 of 19 | ENST00000425673.6 | NP_073746.2 | |
PLEKHG2 | NM_001351694.2 | c.122C>T | p.Pro41Leu | missense_variant | Exon 3 of 18 | NP_001338623.1 | ||
PLEKHG2 | NM_001351693.2 | c.110-165C>T | intron_variant | Intron 2 of 19 | NP_001338622.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152196Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000221 AC: 5AN: 226310Hom.: 0 AF XY: 0.0000323 AC XY: 4AN XY: 123948
GnomAD4 exome AF: 0.000145 AC: 209AN: 1444000Hom.: 0 Cov.: 31 AF XY: 0.000135 AC XY: 97AN XY: 715964
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.122C>T (p.P41L) alteration is located in exon 3 (coding exon 2) of the PLEKHG2 gene. This alteration results from a C to T substitution at nucleotide position 122, causing the proline (P) at amino acid position 41 to be replaced by a leucine (L). 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