10-113766687-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001395068.1(PLEKHS1):c.193C>T(p.His65Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000048 in 1,459,346 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H65Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001395068.1 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 |
---|---|---|---|---|---|---|---|---|
PLEKHS1 | NM_001395068.1 | c.193C>T | p.His65Tyr | missense_variant | Exon 4 of 13 | ENST00000694986.1 | NP_001381997.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLEKHS1 | ENST00000694986.1 | c.193C>T | p.His65Tyr | missense_variant | Exon 4 of 13 | NM_001395068.1 | ENSP00000511629.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000805 AC: 2AN: 248564Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134156
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1459346Hom.: 0 Cov.: 31 AF XY: 0.00000551 AC XY: 4AN XY: 725732
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.175C>T (p.H59Y) alteration is located in exon 3 (coding exon 3) of the PLEKHS1 gene. This alteration results from a C to T substitution at nucleotide position 175, causing the histidine (H) at amino acid position 59 to be replaced by a tyrosine (Y). 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