NM_017780.3(CHD7):c.1666-3238A>G AND Scoliosis, idiopathic 3

Clinical significance:Uncertain significance (Last evaluated: Oct 15, 2013)

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000002108.6

Allele description [Variation Report for NM_017780.3(CHD7):c.1666-3238A>G]

NM_017780.3(CHD7):c.1666-3238A>G

Gene:
CHD7:chromodomain helicase DNA binding protein 7 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
8q12.2
Genomic location:
Preferred name:
NM_017780.3(CHD7):c.1666-3238A>G
HGVS:
  • NC_000008.11:g.60777762A>G
  • NG_007009.1:g.103983A>G
  • NM_017780.3:c.1666-3238A>G
  • LRG_176t1:c.1666-3238A>G
  • LRG_176:g.103983A>G
  • NC_000008.10:g.61690321A>G
  • NM_017780.2:c.1666-3238A>G
Nucleotide change:
A-G (rs4738824)
Links:
OMIM: 608892.0009; dbSNP: rs4738824
NCBI 1000 Genomes Browser:
rs4738824
Molecular consequence:
  • NM_017780.3:c.1666-3238A>G - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Scoliosis, idiopathic 3 (IS3)
Synonyms:
SCOLIOSIS, ISOLATED, SUSCEPTIBILITY TO, 3
Identifiers:
MedGen: C1837461; OMIM: 608765

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000022266OMIMno assertion criteria providedUncertain significance
(Oct 15, 2013)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

CHD7 gene polymorphisms and familial idiopathic scoliosis.

Tilley MK, Justice CM, Swindle K, Marosy B, Wilson AF, Miller NH.

Spine (Phila Pa 1976). 2013 Oct 15;38(22):E1432-6. doi: 10.1097/BRS.0b013e3182a51781.

PubMed [citation]
PMID:
23883829
PMCID:
PMC3881965

CHD7 gene polymorphisms are associated with susceptibility to idiopathic scoliosis.

Gao X, Gordon D, Zhang D, Browne R, Helms C, Gillum J, Weber S, Devroy S, Swaney S, Dobbs M, Morcuende J, Sheffield V, Lovett M, Bowcock A, Herring J, Wise C.

Am J Hum Genet. 2007 May;80(5):957-65. Epub 2007 Mar 12.

PubMed [citation]
PMID:
17436250
PMCID:
PMC1852746

Details of each submission

From OMIM, SCV000022266.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

This variant, formerly titled SCOLIOSIS, IDIOPATHIC, SUSCEPTIBILITY TO, 3, has been reclassified based on the findings of Tilley et al. (2013).

To search for genes underlying susceptibility to idiopathic scoliosis (see IS3, 608765), Gao et al. (2007) ascertained a cohort of 52 families and conducted a study by genomewide scans, which produced evidence of linkage in association with 8q12 loci (multipoint lod = 2.77; p = 0.0028). Further mapping in the region showed significant evidence of disease-associated haplotypes centering over exons 2 through 4 of the CHD7 gene, which is associated with the CHARGE syndrome of multiple developmental anomalies. In 25 affected probands with idiopathic scoliosis (see IS3, 608765) and 44 parental controls, Gao et al. (2007) identified a single-nucleotide polymorphism, SNP rs4738824, an A-to-G change in intron 2 of the CHD7 gene that was predicted to disrupt a caudal-type (cdx) transcription factor binding site. The A nucleotide of this SNP appears to be perfectly conserved across 9 vertebrate species. In the 27 remaining families in the study, Gao et al. (2007) found significant overtransmission of the G allele, which was predicted to disrupt a caudal-type (cdx) transcription factor binding site, to affected offspring (p = 0.005).

Tilley et al. (2013) performed model-independent linkage analysis and tests of association for 22 single-nucleotide polymorphisms in the CHD7 gene in 244 families of European descent with familial idiopathic scoliosis. Linkage analysis identified 3 marginally significant results. However, their results were not significant for tests of association to the CHD7 gene (p less than 0.01). In addition, no significant results (p less than 0.01) were found from a metaanalysis of the results from the tests of association from their sample and that of Gao et al. (2007).

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

Last Updated: Mar 30, 2019

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