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NM_006892.4(DNMT3B):c.2421-11G>A AND Immunodeficiency-centromeric instability-facial anomalies syndrome 1

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 29, 1999
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:
RCV000007133.7

Allele description [Variation Report for NM_006892.4(DNMT3B):c.2421-11G>A]

NM_006892.4(DNMT3B):c.2421-11G>A

Gene:
DNMT3B:DNA methyltransferase 3 beta [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
20q11.21
Genomic location:
Preferred name:
NM_006892.4(DNMT3B):c.2421-11G>A
HGVS:
  • NC_000020.11:g.32807751G>A
  • NG_007290.1:g.50367G>A
  • NM_001207055.2:c.2046-11G>A
  • NM_001207056.2:c.1944-11G>A
  • NM_006892.4:c.2421-11G>AMANE SELECT
  • NM_175848.2:c.2361-11G>A
  • NM_175849.2:c.2172-11G>A
  • NM_175850.3:c.2397-11G>A
  • LRG_56:g.50367G>A
  • NC_000020.10:g.31395557G>A
  • NM_175850.2:c.2397-11G>A
Note:
NCBI staff reviewed the sequence information reported in PubMed 10555141 Fig. 8D to determine the location of this allele on the current reference sequence.
Nucleotide change:
IVS22AS, G-A, -11
Links:
OMIM: 602900.0009; dbSNP: rs547940069
NCBI 1000 Genomes Browser:
rs547940069
Molecular consequence:
  • NM_001207055.2:c.2046-11G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001207056.2:c.1944-11G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_006892.4:c.2421-11G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_175848.2:c.2361-11G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_175849.2:c.2172-11G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_175850.3:c.2397-11G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Immunodeficiency-centromeric instability-facial anomalies syndrome 1 (ICF1)
Identifiers:
MONDO: MONDO:0009454; MedGen: C4551557; Orphanet: 2268; OMIM: 242860

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000027329OMIM
no assertion criteria provided
Pathogenic
(Oct 29, 1999) 		germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

X inactivation-specific methylation of LINE-1 elements by DNMT3B: implications for the Lyon repeat hypothesis.

Hansen RS.

Hum Mol Genet. 2003 Oct 1;12(19):2559-67. Epub 2003 Aug 12.

PubMed [citation]
PMID:
12925568

DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development.

Okano M, Bell DW, Haber DA, Li E.

Cell. 1999 Oct 29;99(3):247-57.

PubMed [citation]
PMID:
10555141
See all PubMed Citations (3)

Details of each submission

From OMIM, SCV000027329.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

For discussion of the splice site mutation in the DNMT3B gene that was found in compound heterozygous state in a patient with ICF syndrome (ICF1; 242860) by Okano et al. (1999), see 602900.0008.

Hansen et al. (1999) described this mutation in homozygous state in 1 family and in compound heterozygous state in a second family in which it was combined with the A603T mutation (602900.0008). Hansen et al. (1999) referred to this mutation as IVS21-11G-A. It appeared that Okano et al. (1999) and Hansen et al. (1999) were studying the same patient. The cells from the family were obtained by each investigator, apparently from the Coriell Cell Repositories in Camden, New Jersey (GM08728), this being the family described by Carpenter et al. (1988).

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

Last Updated: Sep 29, 2024