12-41188849-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001164595.2(PDZRN4):āc.394G>Cā(p.Gly132Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000269 in 1,261,802 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G132S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001164595.2 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 |
---|---|---|---|---|---|---|---|
PDZRN4 | NM_001164595.2 | c.394G>C | p.Gly132Arg | missense_variant | 1/10 | ENST00000402685.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZRN4 | ENST00000402685.7 | c.394G>C | p.Gly132Arg | missense_variant | 1/10 | 2 | NM_001164595.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000671 AC: 1AN: 148946Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000297 AC: 33AN: 1112856Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 19AN XY: 530482
GnomAD4 genome AF: 0.00000671 AC: 1AN: 148946Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 1AN XY: 72590
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | The c.394G>C (p.G132R) alteration is located in exon 1 (coding exon 1) of the PDZRN4 gene. This alteration results from a G to C substitution at nucleotide position 394, causing the glycine (G) at amino acid position 132 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