rs397514467
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PM5PP3_ModeratePP5
The NM_001104631.2(PDE4D):c.1759A>C(p.Thr587Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T587A) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001104631.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDE4D | NM_001104631.2 | c.1759A>C | p.Thr587Pro | missense_variant | 13/15 | ENST00000340635.11 | NP_001098101.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDE4D | ENST00000340635.11 | c.1759A>C | p.Thr587Pro | missense_variant | 13/15 | 1 | NM_001104631.2 | ENSP00000345502.6 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Acrodysostosis 2 with or without hormone resistance Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 06, 2012 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at