NM_015100.4(POGZ):c.3001C>T (p.Arg1001Ter) AND Intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Apr 11, 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:: RCV000210296.6

Allele description [Variation Report for NM_015100.4(POGZ):c.3001C>T (p.Arg1001Ter)]

NM_015100.4(POGZ):c.3001C>T (p.Arg1001Ter)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

1q21.3

Genomic location:

Preferred name:

NM_015100.4(POGZ):c.3001C>T (p.Arg1001Ter)

HGVS:

NC_000001.11:g.151406034G>A
NG_046601.1:g.58432C>T
NM_001194937.2:c.2974C>T
NM_001194938.2:c.2815C>T
NM_015100.4:c.3001C>TMANE SELECT
NM_145796.4:c.2716C>T
NM_207171.2:c.2842C>T
NP_001181866.1:p.Arg992Ter
NP_001181867.1:p.Arg939Ter
NP_055915.2:p.Arg1001Ter
NP_665739.3:p.Arg906Ter
NP_997054.1:p.Arg948Ter
NC_000001.10:g.151378510G>A
NM_015100.3:c.3001C>T

Protein change:

R1001*; ARG1001TER

Links:

OMIM: 614787.0008; dbSNP: rs869312833

NCBI 1000 Genomes Browser:

rs869312833

Molecular consequence:

NM_001194937.2:c.2974C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001194938.2:c.2815C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_015100.4:c.3001C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_145796.4:c.2716C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_207171.2:c.2842C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000266367	OMIM	no assertion criteria provided	Pathogenic (Mar 29, 2022)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV001983389	GeneReviews	no classification provided	not provided	germline	literature only	PubMed (2) [See all records that cite these PMIDs] 24896178, 31782611
SCV004049790	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	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

SCV000266367

OMIM

no assertion criteria provided

Pathogenic
(Mar 29, 2022)

germline

literature only

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

SCV001983389

GeneReviews

no classification provided

not provided

germline

literature only

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

SCV004049790

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

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	unknown	not provided	not provided	not provided	not provided	not provided	literature only
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Disruption of POGZ Is Associated with Intellectual Disability and Autism Spectrum Disorders.

Stessman HAF, Willemsen MH, Fenckova M, Penn O, Hoischen A, Xiong B, Wang T, Hoekzema K, Vives L, Vogel I, Brunner HG, van der Burgt I, Ockeloen CW, Schuurs-Hoeijmakers JH, Klein Wassink-Ruiter JS, Stumpel C, Stevens SJC, Vles HS, Marcelis CM, van Bokhoven H, Cantagrel V, Colleaux L, et al.

Am J Hum Genet. 2016 Mar 3;98(3):541-552. doi: 10.1016/j.ajhg.2016.02.004.

PubMed [citation]

PMID:: 26942287
PMCID:: PMC4890241

Genome sequencing identifies major causes of severe intellectual disability.

Gilissen C, Hehir-Kwa JY, Thung DT, van de Vorst M, van Bon BW, Willemsen MH, Kwint M, Janssen IM, Hoischen A, Schenck A, Leach R, Klein R, Tearle R, Bo T, Pfundt R, Yntema HG, de Vries BB, Kleefstra T, Brunner HG, Vissers LE, Veltman JA.

Nature. 2014 Jul 17;511(7509):344-7. doi: 10.1038/nature13394. Epub 2014 Jun 4.

PubMed [citation]

PMID:: 24896178

See all PubMed Citations (4)

Details of each submission

From OMIM, SCV000266367.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In 2 unrelated patients with White-Sutton syndrome (WHSUS; 616364), Stessman et al. (2016) identified a de novo heterozygous c.3001C-T transition (c.3001C-T, NM_015100.3) in the POGZ gene, resulting in an arg1001-to-ter (R1001X) substitution. Functional studies of the variant and studies of patient cells were not performed.

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

From GeneReviews, SCV001983389.2

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

Description

Recurrent variant

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

From Genome-Nilou Lab, SCV004049790.1

#	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: Oct 28, 2023

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