chr5-31983522-G-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 1P and 2B. PP2BP4_Moderate
The NM_178140.4(PDZD2):c.844G>C(p.Glu282Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,614,090 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E282A) has been classified as Uncertain significance.
Frequency
Consequence
NM_178140.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDZD2 | NM_178140.4 | c.844G>C | p.Glu282Gln | missense_variant | 3/25 | ENST00000438447.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZD2 | ENST00000438447.2 | c.844G>C | p.Glu282Gln | missense_variant | 3/25 | 1 | NM_178140.4 | P1 | |
PDZD2 | ENST00000502489.5 | n.600G>C | non_coding_transcript_exon_variant | 2/18 | 2 | ||||
PDZD2 | ENST00000513852.1 | n.563G>C | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251288Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135822
GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461892Hom.: 0 Cov.: 32 AF XY: 0.0000344 AC XY: 25AN XY: 727246
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74366
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2022 | The c.844G>C (p.E282Q) alteration is located in exon 2 (coding exon 2) of the PDZD2 gene. This alteration results from a G to C substitution at nucleotide position 844, causing the glutamic acid (E) at amino acid position 282 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