6-150733983-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001029884.3(PLEKHG1):c.302C>T(p.Thr101Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,614,156 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001029884.3 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLEKHG1 | NM_001029884.3 | c.302C>T | p.Thr101Met | missense_variant | 3/17 | ENST00000696526.1 | NP_001025055.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLEKHG1 | ENST00000696526.1 | c.302C>T | p.Thr101Met | missense_variant | 3/17 | NM_001029884.3 | ENSP00000512689 | P1 | ||
PLEKHG1 | ENST00000358517.6 | c.302C>T | p.Thr101Met | missense_variant | 2/16 | 5 | ENSP00000351318 | P1 | ||
PLEKHG1 | ENST00000644968.1 | c.302C>T | p.Thr101Met | missense_variant | 2/16 | ENSP00000496254 | P1 | |||
PLEKHG1 | ENST00000644913.1 | c.518C>T | p.Thr173Met | missense_variant | 2/2 | ENSP00000493494 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251226Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135854
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461862Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727230
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74456
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.302C>T (p.T101M) alteration is located in exon 3 (coding exon 1) of the PLEKHG1 gene. This alteration results from a C to T substitution at nucleotide position 302, causing the threonine (T) at amino acid position 101 to be replaced by a methionine (M). 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