GRCh37/hg19 4q32.1-34.1(chr4:157771352-172496278) AND Autism with high cognitive abilities

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 15, 2021
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:: RCV001352663.1

Allele description [Variation Report for GRCh37/hg19 4q32.1-34.1(chr4:157771352-172496278)]

GRCh37/hg19 4q32.1-34.1(chr4:157771352-172496278)

Genes:

DDX60L:DExD/H-box 60 like [Gene - OMIM - HGNC]
DDX60:DExD/H-box helicase 60 [Gene - OMIM - HGNC]
NEK1:NIMA related kinase 1 [Gene - OMIM - HGNC]
RAPGEF2:Rap guanine nucleotide exchange factor 2 [Gene - OMIM - HGNC]
SH3RF1:SH3 domain containing ring finger 1 [Gene - OMIM - HGNC]
SPOCK3:SPARC (osteonectin), cwcv and kazal like domains proteoglycan 3 [Gene - OMIM - HGNC]
ANP32C:acidic nuclear phosphoprotein 32 family member C [Gene - OMIM - HGNC]
AADAT:aminoadipate aminotransferase [Gene - OMIM - HGNC]
ANXA10:annexin A10 [Gene - OMIM - HGNC]
CBR4:carbonyl reductase 4 [Gene - OMIM - HGNC]
CPE:carboxypeptidase E [Gene - OMIM - HGNC]
CLCN3:chloride voltage-gated channel 3 [Gene - OMIM - HGNC]
C4orf45:chromosome 4 open reading frame 45 [Gene - HGNC]
C4orf46:chromosome 4 open reading frame 46 [Gene - OMIM - HGNC]
ETFDH:electron transfer flavoprotein dehydrogenase [Gene - OMIM - HGNC]
FAM218A:family with sequence similarity 218 member A [Gene - HGNC]
FNIP2:folliculin interacting protein 2 [Gene - OMIM - HGNC]
FSTL5:follistatin like 5 [Gene - HGNC]
GRIA2:glutamate ionotropic receptor AMPA type subunit 2 [Gene - OMIM - HGNC]
GLRB:glycine receptor beta [Gene - OMIM - HGNC]
GASK1B:golgi associated kinase 1B [Gene - HGNC]
HPF1:histone PARylation factor 1 [Gene - OMIM - HGNC]
KLHL2:kelch like family member 2 [Gene - OMIM - HGNC]
MARCHF1:membrane associated ring-CH-type finger 1 [Gene - OMIM - HGNC]
MSMO1:methylsterol monooxygenase 1 [Gene - OMIM - HGNC]
MFAP3L:microfibril associated protein 3 like [Gene - OMIM - HGNC]
NPY1R:neuropeptide Y receptor Y1 [Gene - OMIM - HGNC]
NPY5R:neuropeptide Y receptor Y5 [Gene - OMIM - HGNC]
NAF1:nuclear assembly factor 1 ribonucleoprotein [Gene - OMIM - HGNC]
PALLD:palladin, cytoskeletal associated protein [Gene - OMIM - HGNC]
PPID:peptidylprolyl isomerase D [Gene - OMIM - HGNC]
PDGFC:platelet derived growth factor C [Gene - OMIM - HGNC]
RXFP1:relaxin family peptide receptor 1 [Gene - OMIM - HGNC]
TLL1:tolloid like 1 [Gene - OMIM - HGNC]
TKTL2:transketolase like 2 [Gene - HGNC]
TMA16:translation machinery associated 16 homolog [Gene - HGNC]
TMEM144:transmembrane protein 144 [Gene - HGNC]
TMEM192:transmembrane protein 192 [Gene - HGNC]
TRIM60:tripartite motif containing 60 [Gene - OMIM - HGNC]
TRIM61:tripartite motif containing 61 [Gene - OMIM - HGNC]
LOC101928198:uncharacterized LOC101928198 [Gene]

Variant type:

copy number loss

Cytogenetic location:

4q32.1-34.1

Genomic location:

Chr4: 157771352 - 172496278 (on Assembly GRCh37)

Preferred name:

GRCh37/hg19 4q32.1-34.1(chr4:157771352-172496278)

HGVS:

NC_000004.11:g.(?_157771352)_(172496278_?)del

Condition(s)

Name:: Autism with high cognitive abilities
Identifiers:: MedGen: C4025832; Human Phenotype Ontology: HP:0000753

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001547231	Medical Genetics Laboratory, CHRU Nancy	criteria provided, single submitter (ACMG/ClinGen CNV Guidelines, 2019)	Pathogenic (Mar 15, 2021)	de novo	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

SCV001547231

Medical Genetics Laboratory, CHRU Nancy

criteria provided, single submitter

(ACMG/ClinGen CNV Guidelines, 2019)

Pathogenic
(Mar 15, 2021)

de novo

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	de novo	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen).

Riggs ER, Andersen EF, Cherry AM, Kantarci S, Kearney H, Patel A, Raca G, Ritter DI, South ST, Thorland EC, Pineda-Alvarez D, Aradhya S, Martin CL.

Genet Med. 2020 Feb;22(2):245-257. doi: 10.1038/s41436-019-0686-8. Epub 2019 Nov 6. Erratum in: Genet Med. 2021 Nov;23(11):2230. doi: 10.1038/s41436-021-01150-9.

PubMed [citation]

PMID:: 31690835
PMCID:: PMC7313390

Details of each submission

From Medical Genetics Laboratory, CHRU Nancy, SCV001547231.1

#	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	de novo	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 23, 2022

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