X-153804122-G-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001303512.2(PDZD4):āc.1559C>Gā(p.Pro520Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000209 in 1,150,636 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 69 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P520H) has been classified as Likely benign.
Frequency
Consequence
NM_001303512.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDZD4 | NM_001303512.2 | c.1559C>G | p.Pro520Arg | missense_variant | 8/8 | ENST00000393758.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZD4 | ENST00000393758.7 | c.1559C>G | p.Pro520Arg | missense_variant | 8/8 | 1 | NM_001303512.2 | P4 | |
PDZD4 | ENST00000164640.8 | c.1541C>G | p.Pro514Arg | missense_variant | 8/8 | 1 | A1 | ||
PDZD4 | ENST00000544474.5 | c.1214C>G | p.Pro405Arg | missense_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000600 AC: 68AN: 113392Hom.: 0 Cov.: 26 AF XY: 0.000507 AC XY: 18AN XY: 35538
GnomAD3 exomes AF: 0.000351 AC: 31AN: 88205Hom.: 0 AF XY: 0.000229 AC XY: 6AN XY: 26181
GnomAD4 exome AF: 0.000166 AC: 172AN: 1037191Hom.: 0 Cov.: 33 AF XY: 0.000153 AC XY: 51AN XY: 334309
GnomAD4 genome AF: 0.000599 AC: 68AN: 113445Hom.: 0 Cov.: 26 AF XY: 0.000506 AC XY: 18AN XY: 35601
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 14, 2023 | The c.1541C>G (p.P514R) alteration is located in exon 8 (coding exon 8) of the PDZD4 gene. This alteration results from a C to G substitution at nucleotide position 1541, causing the proline (P) at amino acid position 514 to be replaced by an arginine (R). 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