chr12-41188859-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001164595.2(PDZRN4):āc.404C>Gā(p.Pro135Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000354 in 1,243,472 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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.404C>G | p.Pro135Arg | missense_variant | 1/10 | ENST00000402685.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZRN4 | ENST00000402685.7 | c.404C>G | p.Pro135Arg | missense_variant | 1/10 | 2 | NM_001164595.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000337 AC: 5AN: 148248Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.0000356 AC: 39AN: 1095116Hom.: 0 Cov.: 29 AF XY: 0.0000345 AC XY: 18AN XY: 521260
GnomAD4 genome AF: 0.0000337 AC: 5AN: 148356Hom.: 0 Cov.: 31 AF XY: 0.0000415 AC XY: 3AN XY: 72330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2023 | The c.404C>G (p.P135R) alteration is located in exon 1 (coding exon 1) of the PDZRN4 gene. This alteration results from a C to G substitution at nucleotide position 404, causing the proline (P) at amino acid position 135 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