12-41189014-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001164595.2(PDZRN4):c.559C>T(p.Leu187Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000244 in 1,556,304 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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.559C>T | p.Leu187Phe | missense_variant | 1/10 | ENST00000402685.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDZRN4 | ENST00000402685.7 | c.559C>T | p.Leu187Phe | missense_variant | 1/10 | 2 | NM_001164595.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000988 AC: 15AN: 151804Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.0000367 AC: 6AN: 163400Hom.: 0 AF XY: 0.0000561 AC XY: 5AN XY: 89064
GnomAD4 exome AF: 0.0000164 AC: 23AN: 1404382Hom.: 0 Cov.: 32 AF XY: 0.0000216 AC XY: 15AN XY: 694994
GnomAD4 genome AF: 0.0000987 AC: 15AN: 151922Hom.: 1 Cov.: 31 AF XY: 0.000108 AC XY: 8AN XY: 74246
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 11, 2023 | The c.559C>T (p.L187F) alteration is located in exon 1 (coding exon 1) of the PDZRN4 gene. This alteration results from a C to T substitution at nucleotide position 559, causing the leucine (L) at amino acid position 187 to be replaced by a phenylalanine (F). 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