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NM_001272071.2(AP1S2):c.1-2A>G AND Pettigrew syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 8, 2020
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001270029.2

Allele description [Variation Report for NM_001272071.2(AP1S2):c.1-2A>G]

NM_001272071.2(AP1S2):c.1-2A>G

Gene:
AP1S2:adaptor related protein complex 1 subunit sigma 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp22.2
Genomic location:
Preferred name:
NM_001272071.2(AP1S2):c.1-2A>G
HGVS:
  • NC_000023.11:g.15852526T>C
  • NG_009274.2:g.7452A>G
  • NM_001272071.2:c.1-2A>GMANE SELECT
  • NM_001368994.1:c.1-2A>G
  • NM_001369007.1:c.1-2A>G
  • NM_001369008.1:c.1-2A>G
  • NM_003916.5:c.1-2A>G
  • NC_000023.10:g.15870649T>C
  • NM_003916.3:c.1-2A>G
Links:
dbSNP: rs1934209113
NCBI 1000 Genomes Browser:
rs1934209113
Molecular consequence:
  • NM_001272071.2:c.1-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001368994.1:c.1-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001369007.1:c.1-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_001369008.1:c.1-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
  • NM_003916.5:c.1-2A>G - splice acceptor variant - [Sequence Ontology: SO:0001574]
Functional consequence:
effect on RNA splicing [Variation Ontology: 0362]

Condition(s)

Name:
Pettigrew syndrome (PGS)
Synonyms:
Syndromic X-linked intellectual disability 5; X-linked intellectual disability-hypotonia-facial dysmorphism-aggressive behavior syndrome; X-linked intellectual disability-Dandy-Walker malformation-basal ganglia disease-seizures syndrome
Identifiers:
MONDO: MONDO:0010574; MedGen: C0796254; Orphanet: 1568; Orphanet: 85329; Orphanet: 85335; OMIM: 304340

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001449140Department of Pediatrics, Division of Medical Genetics, Faculty of Medicine Ramathibodi Hospital, Mahidol University
no assertion criteria provided
Pathogenic
(Dec 8, 2020) 		germlineresearch

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
South East Asiangermlineyesnot providednot providednot providednot providednot providedresearch

Details of each submission

From Department of Pediatrics, Division of Medical Genetics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, SCV001449140.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1South East Asiannot providednot providednot providedresearchnot provided

Description

The c.1-2A>G variant in AP1S2 was identified in the patient with Pettigrew syndrome phenotype, and was absent from large population studies (genomAD database). Additionally, in house data indicate that the c.1-2A>G variant has an effect on splicing of AP1S2 gene. In summary, the c.1-2A>G variant meets ACMG criteria to be classified as pathogenic based upon null variant, absent from controls, multiple lines of computational evidence support a deleterious effect on the gene, and patient’s phenotype or family history is highly specific for the disease of Pettigrew syndrome.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jun 23, 2024