11-77336090-A-C
Variant summary
Our verdict is Pathogenic. Variant got 17 ACMG points: 17P and 0B. PM1PM2PM5PP2PP3_ModeratePP5_Very_Strong
The NM_002576.5(PAK1):c.1409T>G(p.Leu470Arg) 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. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L470Q) has been classified as Likely pathogenic.
Frequency
Consequence
NM_002576.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAK1 | NM_002576.5 | c.1409T>G | p.Leu470Arg | missense_variant | 13/15 | ENST00000356341.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAK1 | ENST00000356341.8 | c.1409T>G | p.Leu470Arg | missense_variant | 13/15 | 1 | NM_002576.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 28
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Intellectual developmental disorder with macrocephaly, seizures, and speech delay Pathogenic:2
Likely pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Nov 23, 2023 | Criteria applied: PS2_MOD,PM1,PM5,PS4_SUP,PM2_SUP,PP3; Re-Eval 23.11.2023 RoJ - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Johns Hopkins Genomics, Johns Hopkins University | Jul 09, 2021 | This PAK1 variant is absent from a large population dataset and has not been reported in the literature, to our knowledge. It has an entry in ClinVar. Three bioinformatics tools queried predict that this substitution would be damaging, and the leucine residue at this position is conserved across all vertebrate species assessed. This leucine to arginine substitution is located in PAK1 kinase domain. The crystal structure of the human PAK1 protein shows this residue (Leu470) interacts with the inhibitory switch (IS) domain, which is required for autoinhibition of PAK1 kinase activity. This variant is not predicted to affect normal exon 13 splicing, although this has not been confirmed experimentally to our knowledge. We consider c.1409T>G to be likely pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at