X-153804758-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001303512.2(PDZD4):c.923C>T(p.Pro308Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000182 in 1,097,272 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Consequence
NM_001303512.2 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 | UniProt |
---|---|---|---|---|---|---|---|
PDZD4 | NM_001303512.2 | c.923C>T | p.Pro308Leu | missense_variant | 8/8 | ENST00000393758.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZD4 | ENST00000393758.7 | c.923C>T | p.Pro308Leu | missense_variant | 8/8 | 1 | NM_001303512.2 | P4 | |
PDZD4 | ENST00000164640.8 | c.905C>T | p.Pro302Leu | missense_variant | 8/8 | 1 | A1 | ||
PDZD4 | ENST00000544474.5 | c.578C>T | p.Pro193Leu | missense_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD3 exomes AF: 0.00000550 AC: 1AN: 181911Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67465
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1097272Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 363244
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
Autism Uncertain:1
Uncertain significance, no assertion criteria provided | research | Centre for Addiction & Mental Health, Centre for Addiction & Mental Health | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at