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NM_022552.5(DNMT3A):c.2644C>T (p.Arg882Cys) AND Tatton-Brown-Rahman overgrowth syndrome

Germline classification:
Pathogenic (5 submissions)
Last evaluated:
Sep 8, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000590987.11

Allele description [Variation Report for NM_022552.5(DNMT3A):c.2644C>T (p.Arg882Cys)]

NM_022552.5(DNMT3A):c.2644C>T (p.Arg882Cys)

Gene:
DNMT3A:DNA methyltransferase 3 alpha [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p23.3
Genomic location:
Preferred name:
NM_022552.5(DNMT3A):c.2644C>T (p.Arg882Cys)
HGVS:
  • NC_000002.12:g.25234374G>A
  • NG_029465.2:g.113217C>T
  • NM_001320893.1:c.2188C>T
  • NM_001375819.1:c.1975C>T
  • NM_022552.5:c.2644C>TMANE SELECT
  • NM_153759.3:c.2077C>T
  • NM_175629.2:c.2644C>T
  • NP_001307822.1:p.Arg730Cys
  • NP_001362748.1:p.Arg659Cys
  • NP_072046.2:p.Arg882Cys
  • NP_715640.2:p.Arg693Cys
  • NP_783328.1:p.Arg882Cys
  • LRG_459t1:c.2644C>T
  • LRG_459t2:c.2077C>T
  • LRG_459t4:c.2644C>T
  • LRG_459:g.113217C>T
  • LRG_459p2:p.Arg693Cys
  • LRG_459p4:p.Arg882Cys
  • NC_000002.11:g.25457243G>A
  • NC_000002.11:g.25457243G>A
  • NM_022552.4:c.2644C>T
  • NM_022552.5:c.2644C>T
  • NM_175629.1:c.2644C>T
  • NR_135490.2:n.3074C>T
Protein change:
R659C; ARG822CYS
Links:
OMIM: 602769.0007; dbSNP: rs377577594
NCBI 1000 Genomes Browser:
rs377577594
Molecular consequence:
  • NM_001320893.1:c.2188C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375819.1:c.1975C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_022552.5:c.2644C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_153759.3:c.2077C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_175629.2:c.2644C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_135490.2:n.3074C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
Observations:
1

Condition(s)

Name:
Tatton-Brown-Rahman overgrowth syndrome
Synonyms:
Tatton-Brown-rahman syndrome; Tall stature-intellectual disability-facial dysmorphism syndrome
Identifiers:
MONDO: MONDO:0014382; MedGen: C4014545; Orphanet: 404443; OMIM: 615879

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000700194OMIM
no assertion criteria provided
Pathogenic
(Apr 1, 2022)
unknownliterature only

PubMed (5)
[See all records that cite these PMIDs]

SCV002548850New York Genome Center - CSER-NYCKidSeq
criteria provided, single submitter

(NYGC Assertion Criteria 2020)
Pathogenic
(Aug 5, 2021)
de novoclinical testing

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

Citation Link,

SCV002557964Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 1, 2022)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

SCV003247885Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Sep 8, 2023)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV004847672Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 20, 2019)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedde novoyes1not providednot provided1not providedclinical testing
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedunknownnot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

CLTC as a clinically novel gene associated with multiple malformations and developmental delay.

DeMari J, Mroske C, Tang S, Nimeh J, Miller R, Lebel RR.

Am J Med Genet A. 2016 Apr;170A(4):958-66. doi: 10.1002/ajmg.a.37506. Epub 2016 Jan 29.

PubMed [citation]
PMID:
26822784

DNMT3A mutations in acute myeloid leukemia.

Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE, Kandoth C, Payton JE, Baty J, Welch J, Harris CC, Lichti CF, Townsend RR, Fulton RS, Dooling DJ, Koboldt DC, Schmidt H, Zhang Q, Osborne JR, Lin L, O'Laughlin M, McMichael JF, et al.

N Engl J Med. 2010 Dec 16;363(25):2424-33. doi: 10.1056/NEJMoa1005143. Epub 2010 Nov 10.

PubMed [citation]
PMID:
21067377
PMCID:
PMC3201818
See all PubMed Citations (12)

Details of each submission

From OMIM, SCV000700194.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (5)

Description

Tatton-Brown-Rahman Syndrome

In a patient with Tatton-Brown-Rahman syndrome (TBRS; 615879), Shen et al. (2017) identified a c.2644C-T transition (c.2644C-T, NM_175629.2) in the DNMT3A gene, resulting in an arg882-to-cys (R882C) substitution.

In an 19-year-old Dutch boy with TBRS who developed FAB type M5 acute myelogenous leukemia (AML; 601626) at age 15 years, Hollink et al. (2017) identified a de novo heterozygous germline c.2644C-T transition in the DNMT3A gene, resulting in an arg882-to-cys (R882C) substitution. The mutation was found by whole-exome sequencing and confirmed by Sanger sequencing. Analysis of leukemic cells showed an aberrant karyotype and a somatic PTPN11 mutation (T73I; 176876.0011), but no additional somatic mutations or loss of heterozygosity of the DNMT3A gene. Hollink et al. (2017) suggested that mutations at the R882 residue, which are associated with acute myeloid leukemia in the somatic state, may also predispose germline carriers of the mutation to the development of AML. The authors postulated epigenetic dysregulation as a possible molecular mechanism and suggested that patients with TBRS be followed for hematologic malignancies. Functional studies of the variants were not performed.

In a 6-year-old girl (patient 5) with TBRS, Balci et al. (2020) identified heterozygosity for the recurrent R882C mutation in the DNMT3A gene. The child was previously reported by DeMari et al. (2016) at age 3.5 years with a heterozygous frameshift mutation in the CLTC gene (118955.0001) and a diagnosis of global developmental delay (MRD56; 617854). At age 6 years, the child presented with lymphadenopathy, a mediastinal mass, and hypercalcemia, and was diagnosed with T-cell lymphoblastic lymphoma.

Acute Myeloid Leukemia, Somatic

Of 62 patients with acute myelogenous leukemia (AML; 601626) who were found to have a somatic mutation in the DNMT3A gene, Ley et al. (2010) found that 7 had a C-to-T transition at a CpG dinucleotide, resulting in an arg882-to-cys (R882C) substitution.

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

From New York Genome Center - CSER-NYCKidSeq, SCV002548850.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (3)

Description

The de novo missense variant c.2644C>T, p.Arg882Cys identified in the DNMT3A gene has been reported in multiple patients with Tatton-Brown-Rahman syndrome (PubMed: 28941052, 28432085, 31961069). This variant has 24 heterozygotes (0.016%) in gnomAD v3.1.1, suggesting moderate allele frequency in the populations represented in this database. However, researchers revealed that the median variant allele fraction in individuals reported in the population database with this variant was ~19%, strongly suggesting that the observed frequencies are confounding somatic variants in individuals with age-related clonal hematopoiesis (PMID: 28229513). In silico algorithms predict a deleterious effect, and the variant resides at the C-5 cytosine-specific DNA methylase (Dnmt) domain of the DNMT3A protein. Based on the available evidence, the de novo missense variant c.2644C>T, p.Arg882Cys in the DNMT3A gene is classified as pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1de novoyes1not providednot provided1not providednot providednot provided

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002557964.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function and gain of function are known mechanisms of disease in this gene and are associated with disease. Loss of function has been associated with Tatton-Brown-Rahman syndrome (MIM#615879) while gain of function has been associated with Heyn-Sproul-Jackson syndrome (MIM#618724) and demonstrated for two missense variants (PMID: 30478443). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to cysteine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (34 heterozygotes, 0 homozygotes). However, it is likely somatic in the majority of those heterozygotes due to the low allele balance. (SP) 0309 - Multiple alternative amino acid changes at the same position have been observed in gnomAD (v2) (highest allele count: 64 heterozygotes, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants. p.Arg882 is well reported to be a hotspot for both germline variants causing TBRS and somatic variants in acute myeloid leukaemia (ClinVar, PMID: 28941052). (SP) 0702 - Other missense variants comparable to the one identified in this case have strong previous evidence for pathogenicity. At least two alternative changes (p.(Arg882His) and p.(Arg882Ser)) have been classified as pathogenic or likely pathogenic by clinical laboratories in ClinVar, and p.(Arg882His) has been reported in several individuals with TBRS or syndromic intellectual disability (DECIPHER, PMIDs: 28941052, 29900417). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as pathogenic by multiple clinical laboratories in ClinVar and observed as de novo in at least seven individuals with TBRS (PMIDs: 28941052, 27317772, 28432085, 29900417). (SP) 1203 - This variant has been shown to be de novo in the proband (parental status confirmed) (by trio analysis). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003247885.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with Tatton-Brown-Rahman syndrome (PMID: 27317772, 28432085). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 375882). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt DNMT3A protein function. Experimental studies have shown that this missense change affects DNMT3A function (PMID: 31620784). For these reasons, this variant has been classified as Pathogenic. This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 882 of the DNMT3A protein (p.Arg882Cys).

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

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV004847672.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

The p.Arg882Cys variant in DNMT3A has been reported as a de novo germline occurrence in 4 individuals with Tatton-Brown-Rahman syndrome, one of who developed acute myeloid leukemia, (Tlemsani 2016, Hollink 2017, Shen 2017) and is one of the most common somatic DNMT3A variants in acute myeloid leukemia. It has also been identified in 3/10364 Ashkenazi Jewish chromosomes by gnomAD (http://gnomad.broadinstitute.org). However, the median variant allele fraction in these individuals was rather low, suggesting they might be associated with age-related clonal hematopoiesis. Computational prediction tools and conservation analysis suggest that this variant may impact the protein, and in vitro functional studies support an impact on protein function (Russler-Germain 2014). An additional variant involving this codon p.Arg882His has been identified in individuals with Tatton Brown-Rahman syndrome and is a commonly identified somatic variant in acute myeloid leukemia. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant Tatton-Brown-Rahman syndrome (also known as tall stature-intellectual disability-facial dysmorphism syndrome). ACMG/AMP Criteria applied: PM6_Strong, PS2, PS3_Moderate, PS4_Moderate, PP3.

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

Last Updated: Sep 29, 2024