12p12.3-p11.23CNV Type: Deletion
Largest CNV size: 8800000 bp
Statistics Box:
Number of Reports: 2
Number of Reports: 2
Summary Information
Deletions in this region containing the SOX5 gene were identified in two individuals with developmental delay and/or intellectual disability.
Additional Locus Information
References
Major Reports
Title
Author, Year
Report Class
CNV Type
An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabili...
Deletion
Haploinsufficiency of SOX5 at 12p12.1 is associated with developmental delays with prominent language delay, behavior problems, and mild dysmorphic...
Deletion
Minor Reports
Title
Author, Year
Report Class
CNV Type
No Minor Reports
Cases
Cohort ID
Author, Year
Descripton
Cohort Size
Diagnosis
Age
Gender
CNV Size
Deletion
Duplication
Total CNV's
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
7716711
1
0
1
lamb_12_DD/ID_discovery_cases
Subjects referred for clinical molecular cytogenetic testing to Signature Genomic Laboratories, Seattle Children's Hospital, Pittsburgh Cytogenetic Laboratories, Nantes University Hospital, or Hpital Jean Verdier, or through enrollment in Developmental Genome Anatomy Project (DGAP).
14
Developmental delay (DD) and/or intellectual disability (ID). Several cases also display ADHD or autistic beahviors.
Range, 4.5 mos.-11 yrs.
35.71% Male
8800000
2
0
2
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
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
lamb_12_DD/ID_discovery_cases
NA
aCGH, solid phase hybridization
SignatureChip 105K whole-genome array (SignatureChip OS v1), SignatureChip 135K array (SignatureChip OS v2), Agilent 105K, Agilent 180K, Roche NimbleGen 135K, Illumina HumanHap300
FISH
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
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005114
NA
NA
Developmental delay/intellectual disability/ASD
Clinical profile NA
Cognitive profile NA
19295848
27012560
7716713
GRCh38
Deletion
Yes
lamb_12_DD/ID_discovery_cases-subject12
4.5 mos.
F
Developmental delay
Speech delay: NA. Motor delay: NA. Behavioral problems: NA. Hypotonia: none. Seizures: yes. Brain malformations: NA. Other neurological features: intermittent adducted thumbs, constant tongue thrust. Musculoskeletal anomalies: arachnodactyly, hyperconvex nails, deep plantar creases, minimal clinodactyly of 2nd and 3rd toes, hip laxity. Additional features: anteriorly placed anus, deep sacral cleft with sacral dimple, hypoplastic and inverted nipples. Ophthalmologic features: blue sclerae. Dysmorphic features: sparse ahir, low-set ears, familial Darwinian tubercles, small ear lobules, soft cartiliage in ears, minimal synophrys, upslanting palpebral fissures, high and wide nasal bridge, square/tubular nose, long columella, broad nasal tip, short philtrum, broad and short uvula. Growth parameters: weight, 3rd-5th %ile; height, 10th-25th %ile; OFC, <3rd %ile. Family history: maternal half-sibling with developmental delay; maternal family history of learning disability/intellectual disability and psychiatric disease; father has ADHD and aggression; autistic paternal cousin.
Moderate-severe developmental delay
17741531
26539209
8797679
GRCh38
Deletion
Yes
lamb_12_DD/ID_discovery_cases-subject13
7 yrs.
M
Intellectual disability + ADHD
Speech delay: nonverbal, expressive speech disorder. Motor delay: NA. Behavioral problems: ADHD. Hypotonia: yes. Seizures: none. Brain malformations: Chiari I malformation. Other neurological features: speech dyspraxia, moderate-severe bilateral sensorial hearing loss. Musculoskeletal anomalies: slight right palmar crease, prominent fingertip pads, shirt 2nd toes, scoliosis/kyphosis, prominent sternum. Additional features: chronic diarrhea, low-set nipples. Ophthalmologic features: none. Dysmorphic features: mild hair upsweep, protruding and large ears, small nares and alae, downturned upper lip, straight lower lip, malpositioned teeth. Growth parameters: weight, 49th %ile; height, 53rd %ile; OFC, -1 SD. Family history: NA.
Mild intellectual disability; PPVT receptive score of 65 (-2.3 SD)
17741531
26539209
8797679
GRCh38
Deletion
Yes
Controls
No Control Data Available
Cases
Patient ID
Validation Description
Primary Disorder Inheritence
Inheritence
Family Profile
Disease Segregation
Gene Content
Altered Gene Expression
kaminsky_11_DD/ID/ASD_discovery_cases-ISCA00005114
FISH, qPCR, MLPA, aCGH, or standard G-banded chromosome analysis
Unknown
Unknown
Unknown
RN7SL67P,PDCD5P1,RNU6-254P,EEF1A1P4,RNU1-146P,TCP1P3,LINC02468,UBE2L2,ELOCP31,RNU1-149P,LRRC34P1,RPS27P22,MIR920,KNOP1P1,CENPUP2,RNU4-67P,TUBB4BP1,RN7SKP262,TDGP1,MIR4302,BHLHE41,RNA5SP354,PYROXD1,GOLT1B,SPX,GYS2,LDHB,KCNJ8,CMAS,SULT6B2P,SOX5-AS1,LINC00477,RN7SL38P,C12orf77,ETFRF1,KRAS,RASSF8,INTS13,FGFR1OP2,PLEKHA5,AEBP2,LINC02398,PDE3A,SLCO1C1,SLCO1B3,SLCO1B1,SLCO1A2,IAPP,RECQL,ABCC9,ST8SIA1,C2CD5,ETNK1,BCAT1,LRMP,LMNTD1,RASSF8-AS1,ITPR2,TM7SF3,SLCO1B7,SOX5,SSPN,CASC1
lamb_12_DD/ID_discovery_cases-subject12
FISH
Unknown (not maternal)
NDFIP1P1,ZKSCAN7P1,PSMC1P9,CAPZA3,RPL7P6,MEF2BNBP1,RN7SL459P,RN7SL67P,PDCD5P1,RNU6-254P,EEF1A1P4,RNU1-146P,TCP1P3,LINC02468,UBE2L2,ELOCP31,RNU1-149P,LRRC34P1,RPS27P22,MIR920,KNOP1P1,CENPUP2,RNU4-67P,TUBB4BP1,RN7SKP262,TDGP1,MIR4302,BHLHE41,RNA5SP354,PLCZ1,PYROXD1,GOLT1B,SPX,GYS2,LDHB,KCNJ8,CMAS,SULT6B2P,SOX5-AS1,LINC00477,RN7SL38P,C12orf77,ETFRF1,KRAS,RASSF8,RERGL,PIK3C2G,PLEKHA5,AEBP2,LINC02398,PDE3A,SLCO1C1,SLCO1B3,SLCO1B1,SLCO1A2,IAPP,RECQL,ABCC9,ST8SIA1,C2CD5,ETNK1,BCAT1,LRMP,LMNTD1,RASSF8-AS1,ITPR2,SLCO1B7,SOX5,SSPN,CASC1
lamb_12_DD/ID_discovery_cases-subject13
FISH
Unknown
NDFIP1P1,ZKSCAN7P1,PSMC1P9,CAPZA3,RPL7P6,MEF2BNBP1,RN7SL459P,RN7SL67P,PDCD5P1,RNU6-254P,EEF1A1P4,RNU1-146P,TCP1P3,LINC02468,UBE2L2,ELOCP31,RNU1-149P,LRRC34P1,RPS27P22,MIR920,KNOP1P1,CENPUP2,RNU4-67P,TUBB4BP1,RN7SKP262,TDGP1,MIR4302,BHLHE41,RNA5SP354,PLCZ1,PYROXD1,GOLT1B,SPX,GYS2,LDHB,KCNJ8,CMAS,SULT6B2P,SOX5-AS1,LINC00477,RN7SL38P,C12orf77,ETFRF1,KRAS,RASSF8,RERGL,PIK3C2G,PLEKHA5,AEBP2,LINC02398,PDE3A,SLCO1C1,SLCO1B3,SLCO1B1,SLCO1A2,IAPP,RECQL,ABCC9,ST8SIA1,C2CD5,ETNK1,BCAT1,LRMP,LMNTD1,RASSF8-AS1,ITPR2,SLCO1B7,SOX5,SSPN,CASC1
Controls
No Control Data Available
No Animal Model Data Available