NM_002578.5:c.531G>A

Variant names:

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_002578.5(PAK3):c.531G>A(p.Glu177Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00327 in 1,201,610 control chromosomes in the GnomAD database, including 6 homozygotes. There are 1,172 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0024 ( 0 hom., 70 hem., cov: 23)

Exomes 𝑓: 0.0034 ( 6 hom. 1102 hem. )

Consequence

PAK3
NM_002578.5 synonymous

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.612

Publications

2 publications found

Variant links:

Genes affected

PAK3 (HGNC:8592): (p21 (RAC1) activated kinase 3) The protein encoded by this gene is a serine-threonine kinase and forms an activated complex with GTP-bound RAS-like (P21), CDC2 and RAC1. This protein may be necessary for dendritic development and for the rapid cytoskeletal reorganization in dendritic spines associated with synaptic plasticity. Defects in this gene are the cause of a non-syndromic form of X-linked intellectual disability. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2017]

PAK3 Gene-Disease associations (from GenCC):

corpus callosum, agenesis of
Inheritance: XL Classification: DEFINITIVE Submitted by: G2P
intellectual disability, X-linked 30
Inheritance: XL Classification: DEFINITIVE, STRONG, MODERATE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
X-linked syndromic intellectual disability
Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
non-syndromic X-linked intellectual disability
Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

PAK3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant X-111162977-G-A is Benign according to our data. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-111162977-G-A is described in CliVar as Benign/Likely_benign. Clinvar id is 211837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.612 with no splicing effect.

BS2

High Hemizygotes in GnomAd4 at 70 XL gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PAK3	NM_002578.5 link	c.531G>A	p.Glu177Glu	synonymous_variant	Exon 9 of 18	ENST00000372007.10	NP_002569.1	O75914-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PAK3	ENST00000372007.10 link	c.531G>A	p.Glu177Glu	synonymous_variant	Exon 9 of 18	1	NM_002578.5	ENSP00000361077.4		O75914-2

Frequencies

GnomAD3 genomes

AF:

0.00237

AC:

263

AN:

110903

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000425

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00152

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000764

Gnomad FIN

AF:

0.00302

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00426

Gnomad OTH

AF:

0.000676

GnomAD2 exomes

AF:

0.00237

AC:

428

AN:

180542

AF XY:

0.00228

show subpopulations

Gnomad AFR exome

AF:

0.000609

Gnomad AMR exome

AF:

0.000256

Gnomad ASJ exome

AF:

0.00107

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00238

Gnomad NFE exome

AF:

0.00401

Gnomad OTH exome

AF:

0.00289

GnomAD4 exome

AF:

0.00336

AC:

3667

AN:

1090656

Hom.:

Cov.:

AF XY:

0.00309

AC XY:

1102

AN XY:

356658

show subpopulations

African (AFR)

AF:

0.000495

AC:

AN:

26248

American (AMR)

AF:

0.000256

AC:

AN:

35174

Ashkenazi Jewish (ASJ)

AF:

0.00114

AC:

AN:

19322

East Asian (EAS)

AF:

0.0000332

AC:

AN:

30162

South Asian (SAS)

AF:

0.00196

AC:

106

AN:

53957

European-Finnish (FIN)

AF:

0.00220

AC:

AN:

40517

Middle Eastern (MID)

AF:

0.00122

AC:

AN:

4112

European-Non Finnish (NFE)

AF:

0.00394

AC:

3289

AN:

835312

Other (OTH)

AF:

0.00290

AC:

133

AN:

45852

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

120

239

359

478

598

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

124

248

372

496

620

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00237

AC:

263

AN:

110954

Hom.:

Cov.:

AF XY:

0.00210

AC XY:

AN XY:

33270

show subpopulations

African (AFR)

AF:

0.000424

AC:

AN:

30633

American (AMR)

AF:

0.00

AC:

AN:

10359

Ashkenazi Jewish (ASJ)

AF:

0.00152

AC:

AN:

2635

East Asian (EAS)

AF:

0.00

AC:

AN:

3518

South Asian (SAS)

AF:

0.000766

AC:

AN:

2611

European-Finnish (FIN)

AF:

0.00302

AC:

AN:

5963

Middle Eastern (MID)

AF:

0.00

AC:

AN:

218

European-Non Finnish (NFE)

AF:

0.00426

AC:

225

AN:

52835

Other (OTH)

AF:

0.000668

AC:

AN:

1498

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00206

Hom.:

Bravo

AF:

0.00211

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Nov 16, 2017

Athena Diagnostics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Oct 27, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

Jul 06, 2017

Genetic Services Laboratory, University of Chicago

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Intellectual disability, X-linked 30

Benign:1

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

History of neurodevelopmental disorder

Benign:1

Jul 28, 2016

Ambry Genetics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

1.5

(source)

DANN

Benign

0.47

PhyloP100

-0.61

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over