NM_015100.4(POGZ):c.2849dup (p.Val951fs) AND Intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome

Germline classification:: Likely pathogenic (3 submissions)
Last evaluated:: Apr 11, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001269299.4

Allele description [Variation Report for NM_015100.4(POGZ):c.2849dup (p.Val951fs)]

NM_015100.4(POGZ):c.2849dup (p.Val951fs)

Gene:

POGZ:pogo transposable element derived with ZNF domain [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

1q21.3

Genomic location:

Preferred name:

NM_015100.4(POGZ):c.2849dup (p.Val951fs)

HGVS:

NC_000001.11:g.151406188dup
NG_046601.1:g.58280dup
NM_001194937.2:c.2822dup
NM_001194938.2:c.2663dup
NM_015100.4:c.2849dupMANE SELECT
NM_145796.4:c.2564dup
NM_207171.2:c.2690dup
NP_001181866.1:p.Val942fs
NP_001181867.1:p.Val889fs
NP_055915.2:p.Val951fs
NP_665739.3:p.Val856fs
NP_997054.1:p.Val898fs
NC_000001.10:g.151378664dup
NM_015100.3:c.2849dupC
NM_015100.4:c.2849dupCMANE SELECT

Protein change:

V856fs

Links:

dbSNP: rs1653560615

NCBI 1000 Genomes Browser:

rs1653560615

Molecular consequence:

NM_001194937.2:c.2822dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001194938.2:c.2663dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_015100.4:c.2849dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_145796.4:c.2564dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_207171.2:c.2690dup - frameshift variant - [Sequence Ontology: SO:0001589]

Observations:

Condition(s)

Name:: Intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome
Identifiers:: MONDO: MONDO:0014606; MedGen: C4225351; OMIM: 616364

Recent activity

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torsin-1A-interacting protein 2-like [Trichomycterus rosablanca]
torsin-1A-interacting protein 2-like [Trichomycterus rosablanca]
gi|2673051474|ref|XP_062854483.1|

Protein
SET domain-containing protein 4 isoform X2 [Homo sapiens]
SET domain-containing protein 4 isoform X2 [Homo sapiens]
gi|2462582918|ref|XP_054180654.1|

Protein
Homo sapiens ankyrin repeat-containing protein (ANKRD11) mRNA, complete cds
Homo sapiens ankyrin repeat-containing protein (ANKRD11) mRNA, complete cds
gi|38638916|gb|AY373756.1|

Nucleotide
Pmfbp1 polyamine modulated factor 1 binding protein 1 [Mus musculus]
Pmfbp1 polyamine modulated factor 1 binding protein 1 [Mus musculus]
Gene ID:56523

Gene
56523[uid] AND (alive[prop]) (1)
Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001448646	Daryl Scott Lab, Baylor College of Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Nov 11, 2020)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 25741868, 33461977
SCV001527776	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 17, 2018)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004049796	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 11, 2023)	germline	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

SCV001448646

Daryl Scott Lab, Baylor College of Medicine

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Nov 11, 2020)

unknown

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV001527776

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 17, 2018)

unknown

clinical testing

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

SCV004049796

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 11, 2023)

germline

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	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Clinical exome sequencing data reveal high diagnostic yields for congenital diaphragmatic hernia plus (CDH+) and new phenotypic expansions involving CDH.

Scott TM, Campbell IM, Hernandez-Garcia A, Lalani SR, Liu P, Shaw CA, Rosenfeld JA, Scott DA.

J Med Genet. 2022 Mar;59(3):270-278. doi: 10.1136/jmedgenet-2020-107317. Epub 2021 Jan 18.

PubMed [citation]

PMID:: 33461977
PMCID:: PMC8286264

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 Daryl Scott Lab, Baylor College of Medicine, SCV001448646.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (2)

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

From Baylor Genetics, SCV001527776.1

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

Description

This variant was determined to be likely pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

#	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

From Genome-Nilou Lab, SCV004049796.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jul 29, 2024

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