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NM_002578.5(PAK3):c.1282T>A (p.Trp428Arg) AND Intellectual disability, X-linked 30

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Dec 10, 2018
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000824810.1

Allele description [Variation Report for NM_002578.5(PAK3):c.1282T>A (p.Trp428Arg)]

NM_002578.5(PAK3):c.1282T>A (p.Trp428Arg)

Gene:
PAK3:p21 (RAC1) activated kinase 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq23
Genomic location:
Preferred name:
NM_002578.5(PAK3):c.1282T>A (p.Trp428Arg)
HGVS:
  • NC_000023.11:g.111196515T>A
  • NG_008288.2:g.257231T>A
  • NM_001128166.3:c.1282T>A
  • NM_001128167.3:c.1282T>A
  • NM_001128168.3:c.1390T>A
  • NM_001128172.2:c.1345T>A
  • NM_001128173.3:c.1327T>A
  • NM_001324325.2:c.1282T>A
  • NM_001324326.2:c.1282T>A
  • NM_001324327.2:c.1327T>A
  • NM_001324328.2:c.1327T>A
  • NM_001324329.2:c.1327T>A
  • NM_001324330.2:c.1282T>A
  • NM_001324331.2:c.1282T>A
  • NM_001324332.2:c.1282T>A
  • NM_001324333.2:c.1327T>A
  • NM_001324334.2:c.1282T>A
  • NM_002578.5:c.1282T>AMANE SELECT
  • NP_001121638.1:p.Trp428Arg
  • NP_001121639.1:p.Trp428Arg
  • NP_001121640.1:p.Trp464Arg
  • NP_001121644.1:p.Trp449Arg
  • NP_001121645.1:p.Trp443Arg
  • NP_001311254.1:p.Trp428Arg
  • NP_001311255.1:p.Trp428Arg
  • NP_001311256.1:p.Trp443Arg
  • NP_001311257.1:p.Trp443Arg
  • NP_001311258.1:p.Trp443Arg
  • NP_001311259.1:p.Trp428Arg
  • NP_001311260.1:p.Trp428Arg
  • NP_001311261.1:p.Trp428Arg
  • NP_001311262.1:p.Trp443Arg
  • NP_001311263.1:p.Trp428Arg
  • NP_002569.1:p.Trp428Arg
  • NC_000023.10:g.110439743T>A
  • NM_002578.3:c.1282T>A
  • NR_136747.2:n.1711T>A
  • NR_136748.1:n.1457T>A
  • p.W428R
Protein change:
W428R
Links:
dbSNP: rs1603378331
NCBI 1000 Genomes Browser:
rs1603378331
Molecular consequence:
  • NM_001128166.3:c.1282T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001128167.3:c.1282T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001128168.3:c.1390T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001128172.2:c.1345T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001128173.3:c.1327T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324325.2:c.1282T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324326.2:c.1282T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324327.2:c.1327T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324328.2:c.1327T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324329.2:c.1327T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324330.2:c.1282T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324331.2:c.1282T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324332.2:c.1282T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324333.2:c.1327T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001324334.2:c.1282T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002578.5:c.1282T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_136747.2:n.1711T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_136748.1:n.1457T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Functional consequence:
protein loss of function [Variation Ontology: 0043]

Condition(s)

Name:
Intellectual disability, X-linked 30 (XLID30)
Synonyms:
MENTAL RETARDATION, X-LINKED 47; INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED 30
Identifiers:
MONDO: MONDO:0010361; MedGen: C0796237; Orphanet: 777; OMIM: 300558

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000914231Medical Genome Center, National Center of Neurology and Psychiatry
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenic
(Dec 10, 2018) 		inheritedresearch

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
Asianinheritedyes22not providednot providednot providedresearch

Details of each submission

From Medical Genome Center, National Center of Neurology and Psychiatry, SCV000914231.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1Asian2not providednot providedresearchnot provided

Description

X-linked recessive mode

Description

The most severe form of intellectual disability.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot provided2not provided2not provided

Last Updated: Aug 5, 2023