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GM08747 Fibroblast

Description:

IMMUNODEFICIENCY-CENTROMERIC INSTABILITY-FACIAL ANOMALIES SYNDROME
DNA METHYLTRANSFERASE 3B; DNMT3B

Affected:

Yes

Sex:

Female

Age:

1 YR (At Sampling)

  • Overview
  • Characterizations
  • Phenotypic Data
  • Publications
  • External Links
  • Images
  • Culture Protocols

Overview

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Repository NIGMS Human Genetic Cell Repository
Subcollection Chromosome Abnormalities
Class Syndromes with Increased Chromosome Breakage
Cell Type Fibroblast
Transformant Untransformed
Race White
Family Member 1
Relation to Proband proband
Confirmation Clinical summary/Case history
Species Homo sapiens
Common Name Human
Remarks Instability of heterochromatin of chromosomes #1, #9, and #16 with variable combined immunodeficiency; dysmorphic facial features, developmental delay, malabsorption, and recurrent infections; see GM08714 Lymphoid; 46,XX in fibroblasts; donor subject is a compound heterozygote: one allele has a G>A transition at nucleotide 1807 (1807G>A) of the DNMT3B gene resulting in an Ala to Thr substitution at codon 603 [Ala603Thr (A603T)], the mutation occurring in a region between motifs I and IV within the catalytic domain of DNMT3B; the second allele has a G>A transition within intron 22 located 11 nucleotides 5-prime of the normal splice acceptor site [IVS22AS,G>A,-11] resulting in the generation of a novel splice acceptor site and a 9-bp insertion in the processed RNA. This results in the insertion of 3 amino acids (serine, threonine, and proline) at codon 744 (744ins3). The insertion was within the conserved region of the catalytic domain, which is likely to be disrupted by the insertion of a proline residue. This mutation was de novo.

Characterizations

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PDL at Freeze 6.89
Passage Frozen 9
 
IDENTIFICATION OF SPECIES OF ORIGIN Species of Origin Confirmed by Nucleoside Phosphorylase, Glucose-6-Phosphate Dehydrogenase, and Lactate Dehydrogenase Isoenzyme Electrophoresis and by Chromosome Analysis
 
Gene DNMT3B
Chromosomal Location 20q11.2
Allelic Variant 1 602900.0008; ICF SYNDROME
Identified Mutation ALA603THR; In a patient with ICF syndrome (242860), Okano et al. (1999) found compound heterozygosity for 2 mutations in the DNMT3B gene. The first was a G-to-A transition at nucleotide 1807, resulting in an ala603-to-thr substitution; this change was present in the proband and her mother. The mutation occurred in a region between motifs I and IV, within the catalytic domain of DNMT3B. The second heterozygous mutation was a G-to-A transition within intron 22, located 11 nucleotides 5-prime of the normal splice acceptor site (602900.0009). This mutation resulted in the generation of a novel splice acceptor site and a 9-bp insertion in the processed RNA, encoding 3 amino acids (serine, threonine, and proline) at codon 744. The insertion was within the conserved region of the catalytic domain, which is likely to be disrupted by the insertion of a proline residue. This mutation was de novo.
 
Gene DNMT3B
Chromosomal Location 20q11.2
Allelic Variant 2 602900.0009; ICF SYNDROME
Identified Mutation IVS22AS,G>A,-11; In a patient with ICF syndrome (242860), Okano et al. (1999) found compound heterozygosity for 2 mutations in the DNMT3B gene. The first was a G-to-A transition at nucleotide 1807, resulting in an ala603-to-thr substitution; this change was present in the proband and her mother. The mutation occurred in a region between motifs I and IV, within the catalytic domain of DNMT3B. The second heterozygous mutation was a G-to-A transition within intron 22, located 11 nucleotides 5-prime of the normal splice acceptor site (602900.0009). This mutation resulted in the generation of a novel splice acceptor site and a 9-bp insertion in the processed RNA, encoding 3 amino acids (serine, threonine, and proline) at codon 744. The insertion was within the conserved region of the catalytic domain, which is likely to be disrupted by the insertion of a proline residue. This mutation was de novo.

Phenotypic Data

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Remarks Instability of heterochromatin of chromosomes #1, #9, and #16 with variable combined immunodeficiency; dysmorphic facial features, developmental delay, malabsorption, and recurrent infections; see GM08714 Lymphoid; 46,XX in fibroblasts; donor subject is a compound heterozygote: one allele has a G>A transition at nucleotide 1807 (1807G>A) of the DNMT3B gene resulting in an Ala to Thr substitution at codon 603 [Ala603Thr (A603T)], the mutation occurring in a region between motifs I and IV within the catalytic domain of DNMT3B; the second allele has a G>A transition within intron 22 located 11 nucleotides 5-prime of the normal splice acceptor site [IVS22AS,G>A,-11] resulting in the generation of a novel splice acceptor site and a 9-bp insertion in the processed RNA. This results in the insertion of 3 amino acids (serine, threonine, and proline) at codon 744 (744ins3). The insertion was within the conserved region of the catalytic domain, which is likely to be disrupted by the insertion of a proline residue. This mutation was de novo.

Publications

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Yehezkel S, Segev Y, Viegas-Péquignot E, Skorecki K, Selig S, Hypomethylation of subtelomeric regions in ICF syndrome is associated with abnormally short telomeres and enhanced transcription from telomeric regions Human molecular genetics: 2008
PubMed ID: 18558631
 
Weisenberger DJ, Velicescu M, Cheng JC, Gonzales FA, Liang G, Jones PA, Role of the DNA methyltransferase variant DNMT3b3 in DNA methylation. Mol Cancer Res2(1):62-72 2004
PubMed ID: 14757847
 
Hansen RS, Wijmenga C, Luo P, Stanek AM, Canfield TK, Weemaes CM, Gartler SM, The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome. Proc Natl Acad Sci U S A96:14412-7 1999
PubMed ID: 10588719
 
Okano M, Bell DW, Haber DA, Li E, DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell99(3):247-57 1999
PubMed ID: 10555141

External Links

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dbSNP dbSNP ID: 18945
Gene Cards DNMT3B
Gene Ontology GO:0003677 DNA binding
GO:0003886 DNA (cytosine-5-)-methyltransferase activity
GO:0005634 nucleus
GO:0006306 DNA methylation
GO:0008326 site-specific DNA-methyltransferase (cytosine-specific) activity
GO:0016740 transferase activity
NCBI Gene Gene ID:1789
NCBI GTR 242860 IMMUNODEFICIENCY-CENTROMERIC INSTABILITY-FACIAL ANOMALIES SYNDROME 1; ICF1
602900 DNA METHYLTRANSFERASE 3B; DNMT3B
OMIM 242860 IMMUNODEFICIENCY-CENTROMERIC INSTABILITY-FACIAL ANOMALIES SYNDROME 1; ICF1
602900 DNA METHYLTRANSFERASE 3B; DNMT3B
Omim Description CENTROMERIC INSTABILITY, IMMUNODEFICIENCY SYNDROME; CIID
  ICF SYNDROME
  IMMUNE DEFICIENCY, VARIABLE, WITH CENTROMERIC INSTABILITY OF CHROMOSOMES1, 9, AND 16
  IMMUNODEFICIENCY SYNDROME, VARIABLE
  IMMUNODEFICIENCY-CENTROMERIC INSTABILITY-FACIAL ANOMALIES SYNDROME

Images

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View karyotype 

Culture Protocols

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Passage Frozen 9
Split Ratio 1:3
Temperature 37 C
Percent CO2 5%
Percent O2 AMBIENT
Medium Eagles Minimum Essential Medium with Earle's salts:Dulbecco's modified MEM with 2mM L-glutamine or equivalent
Serum 15% fetal bovine serum Not inactivated
Supplement -
Pricing
International/Commercial/For-profit:
$373.00USD
U.S. Academic/Non-profit/Government:
$216.00USD
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