X-153804153-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001303512.2(PDZD4):c.1528C>T(p.Arg510Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000138 in 1,161,601 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001303512.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDZD4 | ENST00000393758.7 | c.1528C>T | p.Arg510Trp | missense_variant | Exon 8 of 8 | 1 | NM_001303512.2 | ENSP00000377355.3 | ||
PDZD4 | ENST00000164640.8 | c.1510C>T | p.Arg504Trp | missense_variant | Exon 8 of 8 | 1 | ENSP00000164640.4 | |||
PDZD4 | ENST00000544474.5 | c.1183C>T | p.Arg395Trp | missense_variant | Exon 6 of 6 | 1 | ENSP00000442033.1 |
Frequencies
GnomAD3 genomes AF: 0.00000884 AC: 1AN: 113121Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 35267
GnomAD3 exomes AF: 0.00000946 AC: 1AN: 105739Hom.: 0 AF XY: 0.0000340 AC XY: 1AN XY: 29403
GnomAD4 exome AF: 0.0000143 AC: 15AN: 1048480Hom.: 0 Cov.: 33 AF XY: 0.0000119 AC XY: 4AN XY: 336544
GnomAD4 genome AF: 0.00000884 AC: 1AN: 113121Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 35267
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1510C>T (p.R504W) alteration is located in exon 8 (coding exon 8) of the PDZD4 gene. This alteration results from a C to T substitution at nucleotide position 1510, causing the arginine (R) at amino acid position 504 to be replaced by a tryptophan (W). 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