11-77336090-A-C

Variant names:

• chr11-77336090-A-C
• rs1942648391
• NM_002576.5:c.1409T>G

Variant summary

Our verdict is Pathogenic. The variant received 17 ACMG points: 17P and 0B. PM1 PM2 PM5 PP2 PP3_Moderate PP5_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: Genomes: not found (cov: 32)
• Consequence: PAK1 NM_002576.5 missense
• Clinical Significance: Likely pathogenic criteria provided, multiple submitters, no conflicts P:2
• Conservation: PhyloP100: 8.95
• Publications: 1 publications found

Genes affected

PAK1 (HGNC:8590): (p21 (RAC1) activated kinase 1) This gene encodes a family member of serine/threonine p21-activating kinases, known as PAK proteins. These proteins are critical effectors that link RhoGTPases to cytoskeleton reorganization and nuclear signaling, and they serve as targets for the small GTP binding proteins Cdc42 and Rac. This specific family member regulates cell motility and morphology. Mutations in this gene have been associated with macrocephaly, seizures, and speech delay. Overexpression of this gene is also reported in many cancer types, and particularly in breast cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2020]

PAK1 Gene-Disease associations (from GenCC):

• intellectual developmental disorder with macrocephaly, seizures, and speech delay

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics

ACMG classification

Our verdict: Pathogenic. The variant received 17 ACMG points.

• PM1: In a helix (size 10) in uniprot entity PAK1_HUMAN there are 5 pathogenic changes around while only 0 benign (100%) in NM_002576.5
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-77336090-A-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 2442056.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP2: Missense variant in the PAK1 gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 21 curated pathogenic missense variants (we use a threshold of 10). The gene has 3 curated benign missense variants. Gene score misZ: 4.0036 (above the threshold of 3.09). Trascript score misZ: 3.8133 (above the threshold of 3.09). GenCC associations: The gene is linked to intellectual developmental disorder with macrocephaly, seizures, and speech delay.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.93
• PP5: Variant 11-77336090-A-C is Pathogenic according to our data. Variant chr11-77336090-A-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 982892.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PAK1	NM_002576.5	c.1409T>G	p.Leu470Arg	missense_variant	Exon 13 of 15	ENST00000356341.8	NP_002567.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PAK1	ENST00000356341.8	c.1409T>G	p.Leu470Arg	missense_variant	Exon 13 of 15	1	NM_002576.5	ENSP00000348696.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Intellectual developmental disorder with macrocephaly, seizures, and speech delay Pathogenic:2

Nov 23, 2023

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Criteria applied: PS2_MOD,PM1,PM5,PS4_SUP,PM2_SUP,PP3; Re-Eval 23.11.2023 RoJ -

Jul 09, 2021

Johns Hopkins Genomics, Johns Hopkins University

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.35	D
BayesDel_noAF	Pathogenic	0.26
CADD	Pathogenic	33
DANN	Uncertain	1.0
DEOGEN2	Benign	0.33	T;T;.;T
Eigen	Pathogenic	0.72
Eigen_PC	Pathogenic	0.75
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.92	D;D;D;D
M_CAP	Uncertain	0.20	D
MetaRNN	Pathogenic	0.93	D;D;D;D
MetaSVM	Benign	-0.34	T
MutationAssessor	Benign	1.7	L;.;L;.
PhyloP100		8.9
PrimateAI	Pathogenic	0.88	D
PROVEAN	Pathogenic	-5.7	D;D;D;D
REVEL	Pathogenic	0.76
Sift	Pathogenic	0.0	D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D
Polyphen		1.0	D;D;D;D
Vest4		0.97
MutPred		0.82		Gain of methylation at L470 (P = 0.0248);Gain of methylation at L470 (P = 0.0248);Gain of methylation at L470 (P = 0.0248);.;
MVP		0.92
MPC		3.0
ClinPred		0.99	D
GERP RS		5.9
Varity_R		0.95
gMVP		0.97
Mutation Taster		=0/100	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1942648391; hg19: chr11-77047135;