Single allele AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Apr 5, 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:: RCV000677918.2

Allele description [Variation Report for Single allele]

Genes:

CDKN2AIP:CDKN2A interacting protein [Gene - OMIM - HGNC]
FAT1:FAT atypical cadherin 1 [Gene - OMIM - HGNC]
LRP2BP:LRP2 binding protein [Gene - OMIM - HGNC]
PDLIM3:PDZ and LIM domain 3 [Gene - OMIM - HGNC]
RWDD4:RWD domain containing 4 [Gene - HGNC]
UFSP2:UFM1 specific peptidase 2 [Gene - OMIM - HGNC]
WDR17:WD repeat domain 17 [Gene - OMIM - HGNC]
WWC2:WW and C2 domain containing 2 [Gene - OMIM - HGNC]
ZFP42:ZFP42 zinc finger protein [Gene - OMIM - HGNC]
ACSL1:acyl-CoA synthetase long chain family member 1 [Gene - OMIM - HGNC]
ASB5:ankyrin repeat and SOCS box containing 5 [Gene - OMIM - HGNC]
ANKRD37:ankyrin repeat domain 37 [Gene - OMIM - HGNC]
AGA:aspartylglucosaminidase [Gene - OMIM - HGNC]
CASP3:caspase 3 [Gene - OMIM - HGNC]
CENPU:centromere protein U [Gene - OMIM - HGNC]
CFAP96:cilia and flagella associated protein 96 [Gene - HGNC]
CFAP97:cilia and flagella associated protein 97 [Gene - OMIM - HGNC]
CLDN22:claudin 22 [Gene - HGNC]
CLDN24:claudin 24 [Gene - HGNC]
F11:coagulation factor XI [Gene - OMIM - HGNC]
CCDC110:coiled-coil domain containing 110 [Gene - OMIM - HGNC]
CYP4V2:cytochrome P450 family 4 subfamily V member 2 [Gene - OMIM - HGNC]
DCTD:dCMP deaminase [Gene - OMIM - HGNC]
ENPP6:ectonucleotide pyrophosphatase/phosphodiesterase 6 [Gene - OMIM - HGNC]
FAM149A:family with sequence similarity 149 member A [Gene - HGNC]
GPM6A:glycoprotein M6A [Gene - OMIM - HGNC]
HELT:helt bHLH transcription factor [Gene - OMIM - HGNC]
ING2:inhibitor of growth family member 2 [Gene - OMIM - HGNC]
IRF2:interferon regulatory factor 2 [Gene - OMIM - HGNC]
KLKB1:kallikrein B1 [Gene - OMIM - HGNC]
MTNR1A:melatonin receptor 1A [Gene - OMIM - HGNC]
NEIL3:nei like DNA glycosylase 3 [Gene - OMIM - HGNC]
PRIMPOL:primase and DNA directed polymerase [Gene - OMIM - HGNC]
SPCS3:signal peptidase complex subunit 3 [Gene - OMIM - HGNC]
SLC25A4:solute carrier family 25 member 4 [Gene - OMIM - HGNC]
SORBS2:sorbin and SH3 domain containing 2 [Gene - OMIM - HGNC]
SNX25:sorting nexin 25 [Gene - HGNC]
SPATA4:spermatogenesis associated 4 [Gene - OMIM - HGNC]
STOX2:storkhead box 2 [Gene - OMIM - HGNC]
TENM3:teneurin transmembrane protein 3 [Gene - OMIM - HGNC]
TLR3:toll like receptor 3 [Gene - OMIM - HGNC]
TRAPPC11:trafficking protein particle complex subunit 11 [Gene - OMIM - HGNC]
TRIML1:tripartite motif family like 1 [Gene - HGNC]
TRIML2:tripartite motif family like 2 [Gene - OMIM - HGNC]
VEGFC:vascular endothelial growth factor C [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

4q34.1-35.2

Genomic location:

Chr4: 176270886 - 190713650 (on Assembly GRCh37)

HGVS:

NC_000004.11:g.176270886_190713650del

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
SCV000804073	Geisinger Autism and Developmental Medicine Institute, Geisinger Health System	criteria provided, single submitter (ACMG CNV Guidelines, 2011)	Pathogenic (Apr 5, 2018)	paternal	provider interpretation	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000804073

Geisinger Autism and Developmental Medicine Institute, Geisinger Health System

criteria provided, single submitter

(ACMG CNV Guidelines, 2011)

Pathogenic
(Apr 5, 2018)

paternal

provider interpretation

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	paternal	unknown	not provided	not provided	not provided	not provided	not provided	provider interpretation

Citations

PubMed

American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants.

Kearney HM, Thorland EC, Brown KK, Quintero-Rivera F, South ST; Working Group of the American College of Medical Genetics Laboratory Quality Assurance Committee..

Genet Med. 2011 Jul;13(7):680-5. doi: 10.1097/GIM.0b013e3182217a3a.

PubMed [citation]

PMID:: 21681106

Details of each submission

From Geisinger Autism and Developmental Medicine Institute, Geisinger Health System, SCV000804073.2

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

Description

This deletion was identified in a 5 year old male with global developmental delays, mild neuromotor abnormalities, stereotypy, macrocephaly, and large stature. He is monitored for seizures due to spells. He has had normal cardiac echo and ECG, normal cranial ultrasound, normal renal ultrasound (except for a urachal cyst). The deletion was inherited from a father with a history of speech delay, learning disability, bipolar disorder, depression, anxiety, substance abuse, heart murmur, and congenital pancreatic divisum.

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

Last Updated: Oct 14, 2023

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Relating variation to medicine