NM_015100.4(POGZ):c.4103_4104inv (p.Thr1368Lys) AND Inborn genetic diseases

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: May 8, 2017
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:: RCV000623084.11

Allele description [Variation Report for NM_015100.4(POGZ):c.4103_4104inv (p.Thr1368Lys)]

NM_015100.4(POGZ):c.4103_4104inv (p.Thr1368Lys)

Gene:

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

Variant type:

Inversion

Cytogenetic location:

1q21.3

Genomic location:

Preferred name:

NM_015100.4(POGZ):c.4103_4104inv (p.Thr1368Lys)

HGVS:

NC_000001.11:g.151404931_151404932inv
NG_046601.1:g.59534_59535inv
NM_001194937.2:c.4076_4077inv
NM_001194938.2:c.3917_3918inv
NM_015100.4:c.4103_4104invMANE SELECT
NM_145796.4:c.3818_3819inv
NM_207171.2:c.3944_3945inv
NP_001181866.1:p.Thr1359Lys
NP_001181867.1:p.Thr1306Lys
NP_055915.2:p.Thr1368Lys
NP_665739.3:p.Thr1273Lys
NP_997054.1:p.Thr1315Lys
NC_000001.10:g.151377407_151377408inv
NM_015100.3:c.4103_4104delCTinsAG

Protein change:

T1273K

Molecular consequence:

NM_001194937.2:c.4076_4077inv - missense variant - [Sequence Ontology: SO:0001583]
NM_001194938.2:c.3917_3918inv - missense variant - [Sequence Ontology: SO:0001583]
NM_015100.4:c.4103_4104inv - missense variant - [Sequence Ontology: SO:0001583]
NM_145796.4:c.3818_3819inv - missense variant - [Sequence Ontology: SO:0001583]
NM_207171.2:c.3944_3945inv - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Inborn genetic diseases
Identifiers:: MeSH: D030342; MedGen: C0950123

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000742122	Ambry Genetics	criteria provided, single submitter (ambry_reporting_categories_2017)	Uncertain significance (Mar 16, 2017)	germline	clinical testing	PubMed (13) [See all records that cite these PMIDs] 24267886, 22542183, 22495311, 24463507, 24896178, 23375656, 25533962, 25694107, 26739615, 26942287, 27148570, 9862965, 28480548 Citation Link,
SCV000848723	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (May 8, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000742122

Ambry Genetics

criteria provided, single submitter

(ambry_reporting_categories_2017)

Uncertain significance
(Mar 16, 2017)

germline

clinical testing

PubMed (13)
[See all records that cite these PMIDs]

Citation Link,

SCV000848723

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(May 8, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	1	not provided	not provided	1	yes	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism.

Willsey AJ, Sanders SJ, Li M, Dong S, Tebbenkamp AT, Muhle RA, Reilly SK, Lin L, Fertuzinhos S, Miller JA, Murtha MT, Bichsel C, Niu W, Cotney J, Ercan-Sencicek AG, Gockley J, Gupta AR, Han W, He X, Hoffman EJ, Klei L, Lei J, et al.

Cell. 2013 Nov 21;155(5):997-1007. doi: 10.1016/j.cell.2013.10.020.

PubMed [citation]

PMID:: 24267886
PMCID:: PMC3995413

De novo gene disruptions in children on the autistic spectrum.

Iossifov I, Ronemus M, Levy D, Wang Z, Hakker I, Rosenbaum J, Yamrom B, Lee YH, Narzisi G, Leotta A, Kendall J, Grabowska E, Ma B, Marks S, Rodgers L, Stepansky A, Troge J, Andrews P, Bekritsky M, Pradhan K, Ghiban E, Kramer M, et al.

Neuron. 2012 Apr 26;74(2):285-99. doi: 10.1016/j.neuron.2012.04.009.

PubMed [citation]

PMID:: 22542183
PMCID:: PMC3619976

See all PubMed Citations (13)

Details of each submission

From Ambry Genetics, SCV000742122.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	yes	clinical testing	PubMed (13)

Description

Lines of evidence used in support of classification: UNCERTAIN: Alteration(s) of Uncertain Clinical Significance Detected

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

From Ambry Genetics, SCV000848723.5

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

Description

The c.4103_4104delinsAG variant, also known as p.T1368K, is located in coding exon 18 of the POGZ gene, results from an in-frame deletion of CT and insertion of AG at nucleotide positions 4103 to 4104. This results in the substitution of the threonine residue for a lysine residue at codon 1368, an amino acid with similar properties. This amino acid positions are not well conserved in available vertebrate species. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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

Last Updated: Nov 24, 2024

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