NM_001272071.2(AP1S2):c.21del (p.Phe7fs) AND Pettigrew syndrome

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 23, 2023
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:: RCV003153171.1

Allele description [Variation Report for NM_001272071.2(AP1S2):c.21del (p.Phe7fs)]

NM_001272071.2(AP1S2):c.21del (p.Phe7fs)

Gene:

AP1S2:adaptor related protein complex 1 subunit sigma 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

Xp22.2

Genomic location:

Preferred name:

NM_001272071.2(AP1S2):c.21del (p.Phe7fs)

HGVS:

NC_000023.11:g.15852508del
NG_009274.2:g.7474del
NM_001272071.2:c.21delMANE SELECT
NM_001368994.1:c.21del
NM_001369007.1:c.21del
NM_001369008.1:c.21del
NM_003916.5:c.21del
NP_001259000.1:p.Phe7fs
NP_001355923.1:p.Phe7fs
NP_001355936.1:p.Phe7fs
NP_001355937.1:p.Phe7fs
NP_003907.3:p.Phe7fs
NC_000023.10:g.15870631del
NR_160932.1:n.147del
NR_160933.1:n.147del

Protein change:

F7fs

Molecular consequence:

NM_001272071.2:c.21del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001368994.1:c.21del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001369007.1:c.21del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001369008.1:c.21del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003916.5:c.21del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_160932.1:n.147del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_160933.1:n.147del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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

Recent activity

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Mus musculus PAP associated domain containing 4 (Papd4), mRNA
Mus musculus PAP associated domain containing 4 (Papd4), mRNA
gi|19527121|ref|NM_133905.1|

Nucleotide
Mus musculus suppressor of Ty 4 homolog 1 (S. cerevisiae), mRNA (cDNA clone MGC:...
Mus musculus suppressor of Ty 4 homolog 1 (S. cerevisiae), mRNA (cDNA clone MGC:107273 IMAGE:30308013), complete cds
gi|56972237|gb|BC087923.1|

Nucleotide
mitochondrial substrate carrier family protein ucpB isoform X3 [Cucumis sativus]
mitochondrial substrate carrier family protein ucpB isoform X3 [Cucumis sativus]
gi|778727781|ref|XP_011659318.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003842024	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Feb 23, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003842024

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Feb 23, 2023)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From 3billion, SCV003842024.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

The variant is not observed in the gnomAD v2.1.1 dataset. This variant was predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. Therefore, this variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 20, 2023

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