NM_006892.4(DNMT3B):c.2450A>G (p.Asp817Gly) AND Immunodeficiency-centromeric instability-facial anomalies syndrome 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 11, 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:: RCV000007125.3

Allele description [Variation Report for NM_006892.4(DNMT3B):c.2450A>G (p.Asp817Gly)]

NM_006892.4(DNMT3B):c.2450A>G (p.Asp817Gly)

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.2450A>G (p.Asp817Gly)

HGVS:

NC_000020.11:g.32807791A>G
NG_007290.1:g.50407A>G
NM_001207055.2:c.2075A>G
NM_001207056.2:c.1973A>G
NM_006892.4:c.2450A>GMANE SELECT
NM_175848.2:c.2390A>G
NM_175849.2:c.2201A>G
NM_175850.3:c.2426A>G
NP_001193984.1:p.Asp692Gly
NP_001193985.1:p.Asp658Gly
NP_008823.1:p.Asp817Gly
NP_787044.1:p.Asp797Gly
NP_787045.1:p.Asp734Gly
NP_787046.1:p.Asp809Gly
LRG_56:g.50407A>G
NC_000020.10:g.31395597A>G
Q9UBC3:p.Asp817Gly

Protein change:

D658G; ASP809GLY

Links:

UniProtKB: Q9UBC3#VAR_011503; OMIM: 602900.0001; dbSNP: rs121908939

NCBI 1000 Genomes Browser:

rs121908939

Molecular consequence:

NM_001207055.2:c.2075A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001207056.2:c.1973A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_006892.4:c.2450A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_175848.2:c.2390A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_175849.2:c.2201A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_175850.3:c.2426A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

Recent activity

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Actinomyces gaoshouyii strain pika_114 chromosome, complete genome
Actinomyces gaoshouyii strain pika_114 chromosome, complete genome
gi|1172558357|gb|CP020468.1|

Nucleotide
Homo sapiens isolate AP12 toll-like receptor gene, partial cds
Homo sapiens isolate AP12 toll-like receptor gene, partial cds
gi|421954274|gb|JQ481370.1|

Nucleotide
4-hydroxyphenylacetate 3-monooxygenase [Enterobacter hormaechei subsp. hoffmanni...
4-hydroxyphenylacetate 3-monooxygenase [Enterobacter hormaechei subsp. hoffmannii ECNIH3]
gi|682109160|gnl|PRJNA202894|ECNIH3 0|gb|AIN21310.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000027321	OMIM	no assertion criteria provided	Pathogenic (Nov 11, 1999)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000027321

OMIM

no assertion criteria provided

Pathogenic
(Nov 11, 1999)

germline

literature only

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene.

Xu GL, Bestor TH, Bourc'his D, Hsieh CL, Tommerup N, Bugge M, Hulten M, Qu X, Russo JJ, Viegas-Péquignot E.

Nature. 1999 Nov 11;402(6758):187-91.

PubMed [citation]

PMID:: 10647011

Details of each submission

From OMIM, SCV000027321.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a patient with ICF syndrome (ICF1; 242860), Xu et al. (1999) identified a homozygous A-to-G substitution in the DNMT3B gene resulting in an aspartic acid-to-glycine change at codon 809 (D809G). The consanguineous parents were both heterozygous for this mutation. None of 25 normal individuals screened by direct sequencing showed sequence alterations in this region, nor did the mutation occur in a further 30 individuals screened for the AflIII restriction site that is removed by the mutation.

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

Last Updated: Apr 23, 2022

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