NC_000001.10:g.172652343_183538289del10885947 AND 1q24q25 microdeletion syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 6, 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:: RCV000785662.2

Allele description [Variation Report for NC_000001.10:g.172652343_183538289del10885947]

NC_000001.10:g.172652343_183538289del10885947

Genes:

ABL2:ABL proto-oncogene 2, non-receptor tyrosine kinase [Gene - OMIM - HGNC]
BRINP2:BMP/retinoic acid inducible neural specific 2 [Gene - OMIM - HGNC]
COP1:COP1 E3 ubiquitin ligase [Gene - OMIM - HGNC]
DHX9:DExH-box helicase 9 [Gene - OMIM - HGNC]
FAM20B:FAM20B glycosaminoglycan xylosylkinase [Gene - OMIM - HGNC]
GPR52:G protein-coupled receptor 52 [Gene - OMIM - HGNC]
KIAA0040:KIAA0040 [Gene - OMIM - HGNC]
KIAA1614:KIAA1614 [Gene - HGNC]
LHX4:LIM homeobox 4 [Gene - OMIM - HGNC]
NPL:N-acetylneuraminate pyruvate lyase [Gene - OMIM - HGNC]
NPHS2:NPHS2 stomatin family member, podocin [Gene - OMIM - HGNC]
RABGAP1L:RAB GTPase activating protein 1 like [Gene - OMIM - HGNC]
RASAL2:RAS protein activator like 2 [Gene - OMIM - HGNC]
RALGPS2:Ral GEF with PH domain and SH3 binding motif 2 [Gene - OMIM - HGNC]
SEC16B:SEC16 homolog B, endoplasmic reticulum export factor [Gene - OMIM - HGNC]
SHCBP1L:SHC binding and spindle associated 1 like [Gene - OMIM - HGNC]
SMG7:SMG7 nonsense mediated mRNA decay factor [Gene - OMIM - HGNC]
TNFSF18:TNF superfamily member 18 [Gene - OMIM - HGNC]
TNFSF4:TNF superfamily member 4 [Gene - OMIM - HGNC]
ACBD6:acyl-CoA binding domain containing 6 [Gene - OMIM - HGNC]
ANGPTL1:angiopoietin like 1 [Gene - OMIM - HGNC]
ANKRD45:ankyrin repeat domain 45 [Gene - OMIM - HGNC]
DARS2:aspartyl-tRNA synthetase 2, mitochondrial [Gene - OMIM - HGNC]
ASTN1:astrotactin 1 [Gene - OMIM - HGNC]
AXDND1:axonemal dynein light chain domain containing 1 [Gene - HGNC]
CACNA1E:calcium voltage-gated channel subunit alpha1 E [Gene - OMIM - HGNC]
CACYBP:calcyclin binding protein [Gene - OMIM - HGNC]
CENPL:centromere protein L [Gene - OMIM - HGNC]
CEP350:centrosomal protein 350 [Gene - OMIM - HGNC]
FAM163A:family with sequence similarity 163 member A [Gene - OMIM - HGNC]
GLUL:glutamate-ammonia ligase [Gene - OMIM - HGNC]
GAS5:growth arrest specific 5 [Gene - OMIM - HGNC]
IER5:immediate early response 5 [Gene - OMIM - HGNC]
KLHL20:kelch like family member 20 [Gene - OMIM - HGNC]
LAMC1:laminin subunit gamma 1 [Gene - OMIM - HGNC]
LAMC2:laminin subunit gamma 2 [Gene - OMIM - HGNC]
MR1:major histocompatibility complex, class I-related [Gene - OMIM - HGNC]
MRPS14:mitochondrial ribosomal protein S14 [Gene - OMIM - HGNC]
NCF2:neutrophil cytosolic factor 2 [Gene - OMIM - HGNC]
NMNAT2:nicotinamide nucleotide adenylyltransferase 2 [Gene - OMIM - HGNC]
PAPPA2:pappalysin 2 [Gene - OMIM - HGNC]
PRDX6:peroxiredoxin 6 [Gene - OMIM - HGNC]
QSOX1:quiescin sulfhydryl oxidase 1 [Gene - OMIM - HGNC]
RGS16:regulator of G protein signaling 16 [Gene - OMIM - HGNC]
RGS8:regulator of G protein signaling 8 [Gene - OMIM - HGNC]
RGSL1:regulator of G protein signaling like 1 [Gene - OMIM - HGNC]
RNASEL:ribonuclease L [Gene - OMIM - HGNC]
RC3H1:ring finger and CCCH-type domains 1 [Gene - OMIM - HGNC]
SERPINC1:serpin family C member 1 [Gene - OMIM - HGNC]
SLC9C2:solute carrier family 9 member C2 (putative) [Gene - OMIM - HGNC]
SOAT1:sterol O-acyltransferase 1 [Gene - OMIM - HGNC]
STX6:syntaxin 6 [Gene - OMIM - HGNC]
TNN:tenascin N [Gene - OMIM - HGNC]
TNR:tenascin R [Gene - OMIM - HGNC]
TEX35:testis expressed 35 [Gene - HGNC]
TOR1AIP1:torsin 1A interacting protein 1 [Gene - OMIM - HGNC]
TOR1AIP2:torsin 1A interacting protein 2 [Gene - OMIM - HGNC]
TOR3A:torsin family 3 member A [Gene - OMIM - HGNC]
TEDDM1:transmembrane epididymal protein 1 [Gene - OMIM - HGNC]
TDRD5:tudor domain containing 5 [Gene - OMIM - HGNC]
XPR1:xenotropic and polytropic retrovirus receptor 1 [Gene - OMIM - HGNC]
ZBTB37:zinc finger and BTB domain containing 37 [Gene - HGNC]
ZNF648:zinc finger protein 648 [Gene - HGNC]

Variant type:

Deletion

Cytogenetic location:

1q24.3-25.3

Genomic location:

Chr1: 172652343 - 183538289 (on Assembly GRCh37)

Preferred name:

NC_000001.10:g.172652343_183538289del10885947

HGVS:

NC_000001.10:g.172652343_183538289del10885947

Condition(s)

Name:: 1q24q25 microdeletion syndrome
Identifiers:: MedGen: CN252652

Recent activity

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MULTISPECIES: multidrug efflux SMR transporter [Streptomyces]
MULTISPECIES: multidrug efflux SMR transporter [Streptomyces]
gi|490073737|ref|WP_003975912.1|

Protein
dipeptidyl peptidase 9 isoform 1 [Mus musculus]
dipeptidyl peptidase 9 isoform 1 [Mus musculus]
gi|1337002707|ref|NP_001347213.1|

Protein
H.sapiens E4BP4 gene
H.sapiens E4BP4 gene
gi|30955|emb|X64318.1|

Nucleotide
Homo sapiens calcium/calmodulin dependent protein kinase II inhibitor 2 (CAMK2N2...
Homo sapiens calcium/calmodulin dependent protein kinase II inhibitor 2 (CAMK2N2), mRNA
gi|1519244813|ref|NM_033259.3|

Nucleotide
PREDICTED: Homo sapiens ankyrin repeat and MYND domain containing 1 (ANKMY1), tr...
PREDICTED: Homo sapiens ankyrin repeat and MYND domain containing 1 (ANKMY1), transcript variant X28, mRNA
gi|2217328664|ref|XM_047444676.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000863548	Medical Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano	criteria provided, single submitter (ACMG CNV Guidelines, 2011)	Pathogenic (Dec 6, 2018)	de novo	research	PubMed (3) [See all records that cite these PMIDs] 21548129, 26333682, 21681106

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000863548

Medical Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano

criteria provided, single submitter

(ACMG CNV Guidelines, 2011)

Pathogenic
(Dec 6, 2018)

de novo

research

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	de novo	yes	1	not provided	not provided	not provided	not provided	research

Citations

PubMed

Distinctive phenotype in 9 patients with deletion of chromosome 1q24-q25.

Burkardt DD, Rosenfeld JA, Helgeson ML, Angle B, Banks V, Smith WE, Gripp KW, Moline J, Moran RT, Niyazov DM, Stevens CA, Zackai E, Lebel RR, Ashley DG, Kramer N, Lachman RS, Graham JM Jr.

Am J Med Genet A. 2011 Jun;155A(6):1336-51. doi: 10.1002/ajmg.a.34049. Epub 2011 May 5.

PubMed [citation]

PMID:: 21548129
PMCID:: PMC3109510

Two further patients with the 1q24 deletion syndrome expand the phenotype: A possible role for the miR199-214 cluster in the skeletal features of the condition.

Ashraf T, Collinson MN, Fairhurst J, Wang R, Wilson LC, Foulds N.

Am J Med Genet A. 2015 Dec;167A(12):3153-60. doi: 10.1002/ajmg.a.37336. Epub 2015 Sep 3.

PubMed [citation]

PMID:: 26333682

See all PubMed Citations (3)

Details of each submission

From Medical Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, SCV000863548.1

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

#	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		1	not provided	not provided	not provided

Last Updated: Oct 14, 2023

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