Single allele AND Intellectual disability

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Feb 25, 2021
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

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:: RCV001293367.2

Allele description [Variation Report for Single allele]

Genes:

BOK:BCL2 family apoptosis regulator BOK [Gene - OMIM - HGNC]
COPS8:COP9 signalosome subunit 8 [Gene - OMIM - HGNC]
COPS9:COP9 signalosome subunit 9 [Gene - OMIM - HGNC]
D2HGDH:D-2-hydroxyglutarate dehydrogenase [Gene - OMIM - HGNC]
FARP2:FERM, ARH/RhoGEF and pleckstrin domain protein 2 [Gene - OMIM - HGNC]
GPR35:G protein-coupled receptor 35 [Gene - OMIM - HGNC]
ILKAP:ILK associated serine/threonine phosphatase [Gene - OMIM - HGNC]
IQCA1:IQ motif containing with AAA domain 1 [Gene - HGNC]
LRRFIP1:LRR binding FLII interacting protein 1 [Gene - OMIM - HGNC]
NDUFA10:NADH:ubiquinone oxidoreductase subunit A10 [Gene - OMIM - HGNC]
PASK:PAS domain containing serine/threonine kinase [Gene - OMIM - HGNC]
RAB17:RAB17, member RAS oncogene family [Gene - OMIM - HGNC]
RBM44:RNA binding motif protein 44 [Gene - HGNC]
THAP4:THAP domain containing 4 [Gene - OMIM - HGNC]
TRAF3IP1:TRAF3 interacting protein 1 [Gene - OMIM - HGNC]
AGXT:alanine--glyoxylate aminotransferase [Gene - OMIM - HGNC]
ANKMY1:ankyrin repeat and MYND domain containing 1 [Gene - HGNC]
ASB1:ankyrin repeat and SOCS box containing 1 [Gene - OMIM - HGNC]
ANO7:anoctamin 7 [Gene - OMIM - HGNC]
AQP12A:aquaporin 12A [Gene - OMIM - HGNC]
AQP12B:aquaporin 12B [Gene - HGNC]
RNPEPL1:arginyl aminopeptidase like 1 [Gene - OMIM - HGNC]
ACKR3:atypical chemokine receptor 3 [Gene - OMIM - HGNC]
ATG4B:autophagy related 4B cysteine peptidase [Gene - OMIM - HGNC]
CAPN10:calpain 10 [Gene - OMIM - HGNC]
COL6A3:collagen type VI alpha 3 chain [Gene - OMIM - HGNC]
DTYMK:deoxythymidylate kinase [Gene - OMIM - HGNC]
DUSP28:dual specificity phosphatase 28 [Gene - HGNC]
ERFE:erythroferrone [Gene - OMIM - HGNC]
ESPNL:espin like [Gene - OMIM - HGNC]
GAL3ST2:galactose-3-O-sulfotransferase 2 [Gene - OMIM - HGNC]
GPC1:glypican 1 [Gene - OMIM - HGNC]
HES6:hes family bHLH transcription factor 6 [Gene - OMIM - HGNC]
HDLBP:high density lipoprotein binding protein [Gene - OMIM - HGNC]
HDAC4:histone deacetylase 4 [Gene - OMIM - HGNC]
ING5:inhibitor of growth family member 5 [Gene - OMIM - HGNC]
KLHL30:kelch like family member 30 [Gene - HGNC]
KIF1A:kinesin family member 1A [Gene - OMIM - HGNC]
MAB21L4:mab-21 like 4 [Gene - HGNC]
MLPH:melanophilin [Gene - OMIM - HGNC]
MIR149:microRNA 149 [Gene - OMIM - HGNC]
MTERF4:mitochondrial transcription termination factor 4 [Gene - OMIM - HGNC]
NEU4:neuraminidase 4 [Gene - OMIM - HGNC]
OR6B2:olfactory receptor family 6 subfamily B member 2 [Gene - HGNC]
OR6B3:olfactory receptor family 6 subfamily B member 3 [Gene - HGNC]
OTOS:otospiralin [Gene - OMIM - HGNC]
PER2:period circadian regulator 2 [Gene - OMIM - HGNC]
PDCD1:programmed cell death 1 [Gene - OMIM - HGNC]
PRLH:prolactin releasing hormone [Gene - OMIM - HGNC]
PRR21:proline rich 21 [Gene - HGNC]
PPP1R7:protein phosphatase 1 regulatory subunit 7 [Gene - OMIM - HGNC]
RAMP1:receptor activity modifying protein 1 [Gene - OMIM - HGNC]
RTP5:receptor transporter protein 5 (putative) [Gene - HGNC]
SCLY:selenocysteine lyase [Gene - OMIM - HGNC]
SEPTIN2:septin 2 [Gene - OMIM - HGNC]
STK25:serine/threonine kinase 25 [Gene - OMIM - HGNC]
SNED1:sushi, nidogen and EGF like domains 1 [Gene - OMIM - HGNC]
TWIST2:twist family bHLH transcription factor 2 [Gene - OMIM - HGNC]
UBE2F:ubiquitin conjugating enzyme E2 F (putative) [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

2q37.2-37.3

Genomic location:

Chr2: 237201756 - 243048760 (on Assembly GRCh37)

HGVS:

NC_000002.11:g.237201756_243048760del

Observations:

Condition(s)

Name:: Intellectual disability
Synonyms:: Intellectual functioning disability; intellectual disabilities; Intellectual developmental disorder
Identifiers:: MONDO: MONDO:0001071; MeSH: D008607; MedGen: C3714756; Human Phenotype Ontology: HP:0001249

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001481820	Institute of Human Genetics, University of Leipzig Medical Center	no assertion criteria provided	Pathogenic (Feb 25, 2021)	unknown	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001481820

Institute of Human Genetics, University of Leipzig Medical Center

no assertion criteria provided

Pathogenic
(Feb 25, 2021)

unknown

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	1	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001481820.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		1	not provided	not provided	clinical testing	not provided

Description

The copy number variant arr[GRCh37] 2q37.2q37.3(237201756_243048760)x1 was identified in an individual with NDD. Inheritance was not applicable (heterozygous). The variant was reviewed according to current ClinGen recommendations and classified as Pathogenic (criteria: 1A(0), 2A(1), 3C(0.9), 5H(0.3), Total score=2.2).

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

Last Updated: Sep 30, 2023

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