12q13.3-q14.1CNV Type: Deletion
Largest CNV size: 3075222 bp
Statistics Box:
Number of Reports: 4
Number of Reports: 4
Summary Information
Deletions in this region were identified in three individuals with developmental delay and 12q14 microdeletion syndrome.
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
The 12q14 microdeletion syndrome: six new cases confirming the role of HMGA2 in growth.
Deletion
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion
Minor Reports
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
chaves_24_ASD/DD/ID_discovery_cases
CMA read files performed by the Laboratrio Neurogene in Florianpolis, Santa Catarina, Brazil, upon request by medical geneticists and neurologists for investigative/diagnostic purposes, primarily from the Joana de Gusmo Children's Hospital, but also from MDs from the University Hospital Professor Polydoro Ernani de So Thiago and from private clinics in Florianpolis, State of Santa Catarina, betwee
1012
83% of cases presented with developmental delay (DD) and/or intellectual disability (ID), with 33% of cases presented with autism spectrum disorder.
Mean age, 10yrs. (median7.15 yrs., standard deviation10.2).
60.77% Male
1406215
1
0
1
kaminsky_11_DD/ID/ASD_discovery_cases
Cases from the International Standards for Cytogenomic Arrays (ISCA) consortium
15749
Unexplained developmental delay, intellectual disability, dysmorphic features, multiple congenital anomalies, autism spectrum disorders, or clinical features suggestive of a chromosomal syndrome
NA
NA
3232773
1
0
1
lynch_11_DD_discovery_cases
Patients referred with developmental delay for array analysis
2538
Developmental delay (DD)
NA
NA
3075222
3
0
3
maini_18_ASD/DD/ID_discovery_cases
Patients evaluated at the Clinical Genetics Unit of Arcispedale Santa Maria Nuova, AUSL-IRCCS of Reggio Emilia that were investigated through aCGH between 2005 and 2016
293
Cases presented with one or more neurodevelopmental disorders (NDD), multiple congenital anomalies (MCA), and/or dysmorphic features. Most frequent neurodevelopmental diagnoses include language delay (78.5%), intellectual disability (66.4%), motor delay (50.7%), and ASD (13.9%); dysmorphic features were also frequently observed (52.7%)
Mean age, 7 yrs. (range, 1 mo.-29 yrs.)
57.5% Male
2440000
1
0
1
Controls
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
kaminsky_11_DD/ID/ASD_discovery_controls
Controls from the International Standards for Cytogenomic Arrays (ISCA) consortium
10118
Controls
NA
NA
NA
NA
NA
NA
Cases
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
chaves_24_ASD/DD/ID_discovery_cases
Brazil
Array SNP
Affymetrix CytoScan 750K, Affymetrix CytoScan HD
Affymetrix ChAS
kaminsky_11_DD/ID/ASD_discovery_cases
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
FISH, qPCR, MLPA, aCGH, standard G-banded chromosome analysis
lynch_11_DD_discovery_cases
NA
aCGH, array SNP
BlueGenome CytoChip (BACs aCGH), Affymetrix 6.0, Agilent 44K, NimbleGen 135K
BlueFuse for Microarrays V3.4, SignalMap V1.9, DNA Analytics V4.0.76, Genotyping Console V4.0
FISH, qPCR, aCGH (NimbleGen 135K)
maini_18_ASD/DD/ID_discovery_cases
Italian
aCGH, array SNP
Multiple platforms, including Agilent and Affymetrix arrays (8x60K oligochips since 2012)
None
Controls
Cohort ID
Geographical Ancestry
Discovery Method
Platform
Algorithm
Software
Validation Method
kaminsky_11_DD/ID/ASD_discovery_controls
NA
aCGH
Agilent 44K, Agilent 105K
Feature Extraction, DNA Analytics
Cases
Patient ID
Author, Year
Age
Gender
Primary Diagnosis
Clinical Profile
Cognitive Profile
CNV Start
CNV End
CNV Size
Genome Build
Type Method
Validation
chaves_24_ASD/DD/ID_discovery_cases-case720
F
Intellectual disability
Hypotonia, psychiatric disorder, elongated face, oblique palpebral fissures, abnormal lip shape
Moderate intellectual disability
56681775
58087989
1406215
GRCh38
Deletion
No
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005387
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
57041158
60273934
3232777
GRCh38
Deletion
Yes
lynch_11_DD_discovery_cases-case3
6 yrs.
M
Developmental delay
Birth/neonatal history: born at 39 weeks weighing 3.6 kg, feeding difficulties as a neonate. Developmental milestones: moderate global developmental delay; motor delay (walked at 2.5 years of age). Language and communication: no speech at 6 years of age. Motor and musculoskeletal features: small joint hypermobility, poor oromotor control, constant dribbling until 4 years of age. Malformations: pulmonary stenosis, pectus excavatum. Dysmorphic features: long eyelashes, low post hairline, frontal hair whorl, mild brachydactyly. Growth parameters (at 4.5 yrs.): height, 101 cm (-0.6 SD); weight, 15 kg (-1.12 SD); head circumference, 51.5 cm (+0.79 SD).
Moderate global developmental delay
57024248
60099473
3075226
GRCh38
Deletion
Yes
lynch_11_DD_discovery_cases-case5
20 yrs.
M
Developmental delay
Birth/neonatal history: pregnancy complicated by car accident at 28 weeks; born at 36 weeks with birth weight of 2.89 kg; admitted to SCBU overnight, poor feeding as neonate. Developmental milestones: diagnosed with global developmental delay at 8 months; sat at 8 months; walked at 18 months; marked speech delay. Malformations: atrial septal defect that required closure. Dysmorphic features: upslanting palpebral fissures, pinched nose, high palate, flat face, broad hands, flat feet, 2/3 syndactyly. Growth parameters (at 17.7 yrs): height, 161.9 cm (-0.04 SD); weight, 51.1 kg (-0.80 SD); OFC, 53.2 cm (-0.99 SD). Provisional earlier diagnosis of Lujan Fryns.
Moderate developmental delay. Attends special school.
56828289
58117183
1288895
GRCh38
Deletion
Yes
lynch_11_DD_discovery_cases-case6
4 yrs. 4 mos.
M
Developmental delay
Birth/neonatal history: uncomplicated pregnancy; born at term by emergency C-section for fetal distress, weighing 2.85 kg; no feeding problems. Developmental milestones: assessed to have moderate global developmental delay at 4 years 4 months. Langauge and communication: speech delay; unable of putting two words together. Brain MRI: focal cortical dysplasia in insular cortex. Malformations: diagnosis of moderated sub-aortic stenosis at 2.5 years. Vision: hypermetropia. Dysmorphic features: brachycephaly, deep set eyes, bilateral low set posteriorly rotated ears, short nasal bridge with upturned nose, long simple philtrum with thin upper lip. Growth parameters: height, 95 cm (-2.3 SD); weight, 15.1 kg (-1.1 SD); OFC, 49 cm (-2.3 SD). Family history: second child of non-consanguineous parents.
Moderate global developmental delay
56664215
59649466
2985252
GRCh38
Deletion
Yes
maini_18_ASD/DD/ID_discovery_cases-case24
3 yrs.
F
Developmental delay and intellectual disability
Birth history: born at 37 weeks gestation, no reported pregnancy anomalies. Developmental milestones: motor delay, language delay. Language and communication evaluation: absent speech. Musculoskeletal evaluation: pes planus. Behavioral/psychiatric evaluation: no reported behavioral or psychiatric abnormalities. Epilepsy/abnormal EEG: positive for epilepsy and/or abnormal EEG. Additional medical history: neurological anomalies, skin anomalies, ematologic anomalies. Dysmorphic features: straight eyebrows, narrow nasal bridge, large nasal tip, everted lower lip, thin hair, low-set frontal hairline. Growth parameters: microcephaly, normal growth. Family history: negative for consanguineity, positive for familiarity, family history negative for NDDs.
Moderate intellectual disability
57107404
59649074
2541671
GRCh38
Deletion
No
Controls
No Control Data Available
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
chaves_24_ASD/DD/ID_discovery_cases-case720
Unknown
CDK4,CYP27B1,DDIT3,NDUFA4L2,ARHGAP9,SLC26A10,PIP4K2C,INHBE,ATP23,MARCHF9,SDR9C7,ARHGEF25,AGAP2,MBD6,DTX3,B4GALNT1,INHBC,GLI1,STAC3,MIR26A2,RPL13AP23,MIR616,AGAP2-AS1,LRP1,MYO1A,NAB2,MARS1,KIF5A,METTL1,NACA,MIR1228,GIHCG,PRIM1,TSPAN31,MIR6758,MIR6759,LINC02403,LRP1-AS,RN7SKP65,SHMT2,STAT6,TAC3,RNU6-1083P,RNU6-879P,HSD17B6,RDH16,R3HDM2-DT,TSFM,ZBTB39,CTDSP2,OS9,DCTN2,GPR182,AVIL,R3HDM2,NXPH4,PTGES3,EEF1AKMT3,NEMP1
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005387
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
NAB2,MIR1228,NXPH4,SHMT2,NDUFA4L2,RNU6-879P,GLI1,MIR6758,DDIT3,MIR616,PIP4K2C,ARHGEF25,B4GALNT1,RPL13AP23,AGAP2-AS1,TSPAN31,MIR6759,MARCH9,CYP27B1,EEF1AKMT3,RNU6-1083P,MIR26A2,RN7SKP65,LINC02403,RPL21P103,RPS6P22,RNU6-279P,RNU6-871P,LINC02448,RNU4-20P,MYO1A,NEMP1,STAT6,STAC3,INHBC,INHBE,ARHGAP9,MARS,MBD6,KIF5A,DTX3,SLC26A10,OS9,AGAP2,CDK4,METTL1,CTDSP2,LRIG3,LRP1,LRP1-AS,R3HDM2,DCTN2,TSFM,AVIL,ATP23,SLC16A7,LINC02388
lynch_11_DD_discovery_cases-case3
FISH
De novo
NA
Possibly segregated
NAB2,MIR1228,NXPH4,SHMT2,NDUFA4L2,RNU6-879P,GLI1,MIR6758,DDIT3,MIR616,PIP4K2C,ARHGEF25,B4GALNT1,RPL13AP23,AGAP2-AS1,TSPAN31,MIR6759,MARCH9,CYP27B1,EEF1AKMT3,RNU6-1083P,MIR26A2,RN7SKP65,LINC02403,RPL21P103,RPS6P22,RNU6-279P,RNU6-871P,LINC02448,RNU4-20P,MYO1A,NEMP1,STAT6,STAC3,INHBC,INHBE,ARHGAP9,MARS,MBD6,KIF5A,DTX3,SLC26A10,OS9,AGAP2,CDK4,METTL1,CTDSP2,LRIG3,TAC3,LRP1,LRP1-AS,R3HDM2,DCTN2,TSFM,AVIL,ATP23,SLC16A7,LINC02388
lynch_11_DD_discovery_cases-case5
FISH, qPCR
De novo
NA
Possibly segregated
RDH16,GPR182,NAB2,MIR1228,NXPH4,SHMT2,NDUFA4L2,RNU6-879P,GLI1,MIR6758,DDIT3,MIR616,PIP4K2C,ARHGEF25,B4GALNT1,RPL13AP23,AGAP2-AS1,TSPAN31,MIR6759,MARCH9,CYP27B1,EEF1AKMT3,RNU6-1083P,MIR26A2,RN7SKP65,LINC02403,SDR9C7,ZBTB39,MYO1A,NEMP1,STAT6,STAC3,INHBC,INHBE,ARHGAP9,MARS,MBD6,KIF5A,DTX3,SLC26A10,OS9,AGAP2,CDK4,METTL1,CTDSP2,TAC3,LRP1,LRP1-AS,R3HDM2,DCTN2,TSFM,AVIL,ATP23
lynch_11_DD_discovery_cases-case6
aCGH (Nimblegen 135K)
De novo
NA
Possibly segregated
RN7SL809P,RDH16,GPR182,NAB2,MIR1228,NXPH4,SHMT2,NDUFA4L2,RNU6-879P,GLI1,MIR6758,DDIT3,MIR616,PIP4K2C,ARHGEF25,B4GALNT1,RPL13AP23,AGAP2-AS1,TSPAN31,MIR6759,MARCH9,CYP27B1,EEF1AKMT3,RNU6-1083P,MIR26A2,RN7SKP65,LINC02403,RPL21P103,RPS6P22,RNU6-279P,RNU6-871P,LINC02448,RNU4-20P,PTGES3,NACA,PRIM1,SDR9C7,ZBTB39,MYO1A,NEMP1,STAT6,STAC3,INHBC,INHBE,ARHGAP9,MARS,MBD6,KIF5A,DTX3,SLC26A10,OS9,AGAP2,CDK4,METTL1,CTDSP2,LRIG3,HSD17B6,TAC3,LRP1,LRP1-AS,R3HDM2,DCTN2,TSFM,AVIL,ATP23,SLC16A7,LINC02388
maini_18_ASD/DD/ID_discovery_cases-case24
De novo
Simplex
Possibly segregated
MIR1228,NXPH4,SHMT2,NDUFA4L2,RNU6-879P,GLI1,MIR6758,DDIT3,MIR616,PIP4K2C,ARHGEF25,B4GALNT1,RPL13AP23,AGAP2-AS1,TSPAN31,MIR6759,MARCH9,CYP27B1,EEF1AKMT3,RNU6-1083P,MIR26A2,RN7SKP65,LINC02403,RPL21P103,RPS6P22,RNU6-279P,RNU6-871P,LINC02448,RNU4-20P,STAT6,STAC3,INHBC,INHBE,ARHGAP9,MARS,MBD6,KIF5A,DTX3,SLC26A10,OS9,AGAP2,CDK4,METTL1,CTDSP2,LRIG3,LRP1,LRP1-AS,R3HDM2,DCTN2,TSFM,AVIL,ATP23,SLC16A7,LINC02388
Controls
No Control Data Available
No Animal Model Data Available