Single allele AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 2, 2018
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:: RCV000678021.2

Allele description [Variation Report for Single allele]

Genes:

ELF2:E74 like ETS transcription factor 2 [Gene - OMIM - HGNC]
LARP1B:La ribonucleoprotein 1B [Gene - HGNC]
NAA15:N-alpha-acetyltransferase 15, NatA auxiliary subunit [Gene - OMIM - HGNC]
NDUFC1:NADH:ubiquinone oxidoreductase subunit C1 [Gene - OMIM - HGNC]
RAB33B:RAB33B, member RAS oncogene family [Gene - OMIM - HGNC]
SETD7:SET domain containing 7, histone lysine methyltransferase [Gene - OMIM - HGNC]
ABHD18:abhydrolase domain containing 18 [Gene - HGNC]
CLGN:calmegin [Gene - OMIM - HGNC]
C4orf33:chromosome 4 open reading frame 33 [Gene - HGNC]
HSPA4L:heat shock protein family A (Hsp70) member 4 like [Gene - OMIM - HGNC]
INTU:inturned planar cell polarity protein [Gene - OMIM - HGNC]
JADE1:jade family PHD finger 1 [Gene - OMIM - HGNC]
MFSD8:major facilitator superfamily domain containing 8 [Gene - OMIM - HGNC]
MAML3:mastermind like transcriptional coactivator 3 [Gene - OMIM - HGNC]
MGST2:microsomal glutathione S-transferase 2 [Gene - OMIM - HGNC]
MGARP:mitochondria localized glutamic acid rich protein [Gene - OMIM - HGNC]
NOCT:nocturnin [Gene - OMIM - HGNC]
PLK4:polo like kinase 4 [Gene - OMIM - HGNC]
PABPC4L:poly(A) binding protein cytoplasmic 4 like [Gene - HGNC]
PGRMC2:progesterone receptor membrane component 2 [Gene - OMIM - HGNC]
PCDH10:protocadherin 10 [Gene - OMIM - HGNC]
PCDH18:protocadherin 18 [Gene - OMIM - HGNC]
SCOC:short coiled-coil protein [Gene - HGNC]
SCLT1:sodium channel and clathrin linker 1 [Gene - OMIM - HGNC]
SLC25A31:solute carrier family 25 member 31 [Gene - OMIM - HGNC]
SLC7A11:solute carrier family 7 member 11 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

4q28.1-31.1

Genomic location:

Chr4: 126549693 - 141313049 (on Assembly GRCh37)

HGVS:

NC_000004.11:g.126549693_141313049del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: CN517202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000804176	Geisinger Autism and Developmental Medicine Institute, Geisinger Health System	criteria provided, single submitter (ACMG CNV Guidelines, 2011)	Pathogenic (Apr 2, 2018)	unknown	provider interpretation	PubMed (3) [See all records that cite these PMIDs] 24959202, 26446663, 21681106

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000804176

Geisinger Autism and Developmental Medicine Institute, Geisinger Health System

criteria provided, single submitter

(ACMG CNV Guidelines, 2011)

Pathogenic
(Apr 2, 2018)

unknown

provider interpretation

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	provider interpretation

Citations

PubMed

Deletion of 4q28.3-31.23 in the background of multiple malformations with pulmonary hypertension.

Duga B, Czako M, Komlosi K, Hadzsiev K, Torok K, Sumegi K, Kisfali P, Kosztolanyi G, Melegh B.

Mol Cytogenet. 2014;7:36. doi: 10.1186/1755-8166-7-36.

PubMed [citation]

PMID:: 24959202
PMCID:: PMC4066825

Clinical and Molecular Delineation of a Novel De Novo 4q28.3-31.21 Interstitial Deletion in a Patient with Developmental Delay.

Rim JH, Kim SW, Han SH, Yoo J.

Yonsei Med J. 2015 Nov;56(6):1742-4. doi: 10.3349/ymj.2015.56.6.1742. No abstract available.

PubMed [citation]

PMID:: 26446663
PMCID:: PMC4630069

See all PubMed Citations (3)

Details of each submission

From Geisinger Autism and Developmental Medicine Institute, Geisinger Health System, SCV000804176.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	provider interpretation	PubMed (3)

Description

This deletion was identified in a 16 year old male with intellectual disability, seizure disorder, irritability, submucosal cleft palate, microcephaly, short stature, sleep disturbances, and Emery-Driefuss muscular dystrophy. Parental testing was not completed. This region contains at least 36 genes and was also identified on a karyotype. A 16p13.11 intragenic deletion of ABCC6 was also identified through array and a FHL1 likely pathogenic variant identified through a HCM gene panel. Due to its size, this deletion is believed to explain this patient's neurodevelopmental history in combination with his FHL1 mutation.

#	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		not provided	not provided	not provided	not provided

Last Updated: Mar 26, 2023

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