X-153804357-C-G
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001303512.2(PDZD4):āc.1324G>Cā(p.Glu442Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000414 in 1,207,152 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 14 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDZD4 | NM_001303512.2 | c.1324G>C | p.Glu442Gln | missense_variant | 8/8 | ENST00000393758.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZD4 | ENST00000393758.7 | c.1324G>C | p.Glu442Gln | missense_variant | 8/8 | 1 | NM_001303512.2 | P4 | |
PDZD4 | ENST00000164640.8 | c.1306G>C | p.Glu436Gln | missense_variant | 8/8 | 1 | A1 | ||
PDZD4 | ENST00000544474.5 | c.979G>C | p.Glu327Gln | missense_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000221 AC: 25AN: 113301Hom.: 0 Cov.: 25 AF XY: 0.000254 AC XY: 9AN XY: 35437
GnomAD3 exomes AF: 0.0000448 AC: 8AN: 178476Hom.: 0 AF XY: 0.0000153 AC XY: 1AN XY: 65326
GnomAD4 exome AF: 0.0000229 AC: 25AN: 1093851Hom.: 0 Cov.: 33 AF XY: 0.0000139 AC XY: 5AN XY: 360981
GnomAD4 genome AF: 0.000221 AC: 25AN: 113301Hom.: 0 Cov.: 25 AF XY: 0.000254 AC XY: 9AN XY: 35437
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.1306G>C (p.E436Q) alteration is located in exon 8 (coding exon 8) of the PDZD4 gene. This alteration results from a G to C substitution at nucleotide position 1306, causing the glutamic acid (E) at amino acid position 436 to be replaced by a glutamine (Q). 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