chrX-75429082-C-T
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_144969.3(ZDHHC15):c.599G>A(p.Trp200*) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000914 in 1,094,286 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_144969.3 stop_gained
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD4 exome AF: 9.14e-7 AC: 1AN: 1094286Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 360370
GnomAD4 genome Cov.: 23
ClinVar
Submissions by phenotype
Intellectual disability, X-linked 91 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Feb 21, 2018 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. Defects in ZDHHC15 may cause mental retardation, X-linked 91 (MRX91) [MIM:300577]; this is based on the report that loss of ZDHHC15 expression was identified in a woman with a balanced translocation t(X;15)(q13.3;cen) and severe mental retardation [PMID: 15915161] - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at