1-204223481-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_014935.5(PLEKHA6):āc.3136A>Gā(p.Met1046Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000072 in 1,388,652 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 (ā ).
Frequency
Consequence
NM_014935.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLEKHA6 | NM_014935.5 | c.3136A>G | p.Met1046Val | missense_variant | 22/23 | ENST00000272203.8 | NP_055750.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLEKHA6 | ENST00000272203.8 | c.3136A>G | p.Met1046Val | missense_variant | 22/23 | 1 | NM_014935.5 | ENSP00000272203 | P2 | |
PLEKHA6 | ENST00000637508.1 | c.3508A>G | p.Met1170Val | missense_variant | 26/27 | 5 | ENSP00000490182 | A2 | ||
PLEKHA6 | ENST00000414478.1 | c.3196A>G | p.Met1066Val | missense_variant | 22/23 | 5 | ENSP00000402046 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 7.20e-7 AC: 1AN: 1388652Hom.: 0 Cov.: 29 AF XY: 0.00000146 AC XY: 1AN XY: 685664
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 18, 2024 | The c.3136A>G (p.M1046V) alteration is located in exon 22 (coding exon 20) of the PLEKHA6 gene. This alteration results from a A to G substitution at nucleotide position 3136, causing the methionine (M) at amino acid position 1046 to be replaced by a valine (V). 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
Publications
No publications associated with this variant yet.