VCV002762551.1 - ClinVar

NM_022552.5(DNMT3A):c.867_870del (p.Phe290fs)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_022552.5(DNMT3A):c.867_870del (p.Phe290fs)

Variation ID: 2762551 Accession: VCV002762551.1

Type and length

Deletion, 4 bp

Location

Cytogenetic: 2p23.3 2: 25247735-25247738 (GRCh38) [ NCBI UCSC ] 2: 25470604-25470607 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Feb 14, 2024	Feb 14, 2024	Sep 22, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_022552.5:c.867_870del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_072046.2:p.Phe290fs	frameshift
NM_001320893.1:c.411_414del	NP_001307822.1:p.Phe138fs	frameshift
NM_001375819.1:c.198_201del	NP_001362748.1:p.Phe67fs	frameshift
NM_153759.3:c.300_303del	NP_715640.2:p.Phe101fs	frameshift
NM_175629.2:c.867_870del	NP_783328.1:p.Phe290fs	frameshift
NR_135490.2:n.1098_1101del		non-coding transcript variant
NC_000002.12:g.25247735_25247738del
NC_000002.11:g.25470604_25470607del
NG_029465.2:g.99853_99856del
LRG_459:g.99853_99856del
LRG_459t1:c.867_870del	LRG_459p1:p.Phe290Alafs
LRG_459t2:c.300_303del	LRG_459p2:p.Phe101fs
LRG_459t4:c.867_870del	LRG_459p4:p.Phe290fs

... more HGVS ... less HGVS

Protein change

F67fs, F101fs, F138fs, F290fs

Other names

Canonical SPDI

NC_000002.12:25247734:AAAG:

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
DNMT3A		Little evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	762	818

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Tatton-Brown-Rahman overgrowth syndrome	Pathogenic (1)	criteria provided, single submitter	Sep 22, 2023	RCV003584327.2

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Sep 22, 2023)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Tatton-Brown-Rahman overgrowth syndrome Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004327655.1 First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024	Publications: PubMed (1) PubMed: 24614070 Comment: This sequence change creates a premature translational stop signal (p.Phe290Alafs25) in the DNMT3A gene. It is expected to result in an absent or disrupted protein … (more) This sequence change creates a premature translational stop signal (p.Phe290Alafs25) in the DNMT3A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DNMT3A are known to be pathogenic (PMID: 24614070). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with DNMT3A-related conditions. This variant is not present in population databases (gnomAD no frequency). (less)

Comment:

This sequence change creates a premature translational stop signal (p.Phe290Alafs*25) in the DNMT3A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DNMT3A are known to be pathogenic (PMID: 24614070). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant has not been reported in the literature in individuals affected with DNMT3A-related conditions. This variant is not present in population databases (gnomAD no frequency).

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Mutations in the DNA methyltransferase gene DNMT3A cause an overgrowth syndrome with intellectual disability.	Tatton-Brown K	Nature genetics	2014	PMID: 24614070

Text-mined citations for this variant ...

Record last updated Sep 30, 2024

ClinVar Genomic variation as it relates to human health

NM_022552.5(DNMT3A):c.867_870del (p.Phe290fs)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...