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GRCh37/hg19 12q15-21.2(chr12:70084476-77065764)x1 AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 20, 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:
RCV001834178.1

Allele description [Variation Report for GRCh37/hg19 12q15-21.2(chr12:70084476-77065764)x1]

GRCh37/hg19 12q15-21.2(chr12:70084476-77065764)x1

Genes:
  • BBS10:Bardet-Biedl syndrome 10 [Gene - OMIM - HGNC]
  • CNOT2:CCR4-NOT transcription complex subunit 2 [Gene - OMIM - HGNC]
  • GLIPR1:GLI pathogenesis related 1 [Gene - OMIM - HGNC]
  • GLIPR1L1:GLIPR1 like 1 [Gene - OMIM - HGNC]
  • GLIPR1L2:GLIPR1 like 2 [Gene - OMIM - HGNC]
  • KRR1:KRR1 small subunit processome component homolog [Gene - OMIM - HGNC]
  • RAB21:RAB21, member RAS oncogene family [Gene - OMIM - HGNC]
  • RAB3IP:RAB3A interacting protein [Gene - OMIM - HGNC]
  • TBC1D15:TBC1 domain family member 15 [Gene - OMIM - HGNC]
  • THAP2:THAP domain containing 2 [Gene - OMIM - HGNC]
  • ATXN7L3B:ataxin 7 like 3B [Gene - OMIM - HGNC]
  • BEST3:bestrophin 3 [Gene - OMIM - HGNC]
  • CAPS2:calcyphosine 2 [Gene - OMIM - HGNC]
  • LGR5:leucine rich repeat containing G protein-coupled receptor 5 [Gene - OMIM - HGNC]
  • MYRFL:myelin regulatory factor like [Gene - HGNC]
  • NAP1L1:nucleosome assembly protein 1 like 1 [Gene - OMIM - HGNC]
  • OSBPL8:oxysterol binding protein like 8 [Gene - OMIM - HGNC]
  • PHLDA1:pleckstrin homology like domain family A member 1 [Gene - OMIM - HGNC]
  • KCNMB4:potassium calcium-activated channel subfamily M regulatory beta subunit 4 [Gene - OMIM - HGNC]
  • KCNC2:potassium voltage-gated channel subfamily C member 2 [Gene - OMIM - HGNC]
  • PTPRB:protein tyrosine phosphatase receptor type B [Gene - OMIM - HGNC]
  • PTPRR:protein tyrosine phosphatase receptor type R [Gene - OMIM - HGNC]
  • TSPAN8:tetraspanin 8 [Gene - OMIM - HGNC]
  • TRHDE:thyrotropin releasing hormone degrading enzyme [Gene - OMIM - HGNC]
  • TMEM19:transmembrane protein 19 [Gene - HGNC]
  • TPH2:tryptophan hydroxylase 2 [Gene - OMIM - HGNC]
  • ZFC3H1:zinc finger C3H1-type containing [Gene - HGNC]
Variant type:
copy number loss
Cytogenetic location:
12q15-21.2
Genomic location:
Chr12: 70084476 - 77065764 (on Assembly GRCh37)
Preferred name:
GRCh37/hg19 12q15-21.2(chr12:70084476-77065764)x1
HGVS:
NC_000012.11:g.(?_70084476)_(77065764_?)del

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002096462Quest Diagnostics Nichols Institute San Juan Capistrano
no assertion criteria provided
Pathogenic
(Jan 20, 2021) 		germlineclinical testing

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Quest Diagnostics Nichols Institute San Juan Capistrano, SCV002096462.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The copy number loss of 12q15q21.2 involves several coding genes, including CNOT2 (OMIM 604909) and BBS10 (OMIM 610148), and is expected to cause phenotypic and/or developmental abnormalities. This deletion interval overlaps the region of chromosome 12q15 deletion syndrome (OMIM 618608), which is characterized by developmental delay, hypotonia, feeding problems, learning difficulties, nasal speech, skeletal anomalies, and facial dysmorphic features. Some patients may also have congenital heart defects, vision impairment or hypothyroidism. Genotype-phenotype correlation studies have proposed CNOT2 as the critical gene responsible for at least some of the core clinical features of 12q15 microdeletion syndrome, as evidenced by the phenotypic characterization of individuals with truncating variants and focal deletions of this gene (Alesi et al., Am J Med Genet A 2019;179(8):1615-1621, PMID: 31145527; Uehara et al., Am J Med Genet A 2019;179(4):659-662, PMID: 30768759; Uehara et al., Am J Med Genet A 2019;179(12):2506-2509, PMID: 31512373). Additionally, biallelic loss-of-function variants of BBS10 are associated with autosomal recessive Bardet-Biedl syndrome-10 (OMIM 615987), which is characterized by progressive retinal dystrophy, obesity, polydactyly, cognitive impairment, and renal dysplasia.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 11, 2022