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NM_001130823.3(DNMT1):c.3668G>A (p.Arg1223His)

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Interpretation:
Conflicting interpretations of pathogenicity​

Benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
3 (Most recent: Feb 20, 2020)
Last evaluated:
Dec 24, 2018
Accession:
VCV000438391.3
Variation ID:
438391
Description:
single nucleotide variant
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NM_001130823.3(DNMT1):c.3668G>A (p.Arg1223His)

Allele ID
432019
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.2
Genomic location
19: 10140184 (GRCh38) GRCh38 UCSC
19: 10250860 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000019.10:g.10140184C>T
NC_000019.9:g.10250860C>T
NG_028016.3:g.96103G>A
... more HGVS
Protein change
R1223H, R1207H, R1102H
Other names
-
Canonical SPDI
NC_000019.10:10140183:C:T
Functional consequence
variation affecting protein function [Variation Ontology VariO:0003]
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00001
Exome Aggregation Consortium (ExAC) 0.00002
The Genome Aggregation Database (gnomAD), exomes 0.00006
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Links
ClinGen: CA9187695
dbSNP: rs757460628
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 24, 2018 RCV000813215.2
Uncertain significance 1 no assertion criteria provided - RCV000625706.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
DNMT1 - - GRCh38
GRCh37
729 747

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Dec 24, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary sensory neuropathy type IE
Allele origin: germline
Invitae
Accession: SCV000953561.1
Submitted: (Mar 28, 2019)
Evidence details
Comment:
This sequence change replaces arginine with histidine at codon 1223 of the DNMT1 protein (p.Arg1223His). The arginine residue is weakly conserved and there is a … (more)
Benign
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Hereditary sensory neuropathy type IE
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001283153.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (more)
Uncertain significance
(-)
no assertion criteria provided
Method: research
Beckwith-Wiedemann syndrome
Allele origin: germline, not applicable
Genetics and Molecular Pathology Laboratory,Hudson Institute of Medical Research
Accession: SCV000599436.1
Submitted: (Sep 12, 2017)
Evidence details
Comment:
This variant was identified in heterozygous form in 1 of 53 cases with Beckwith Wiedemann syndrome with loss of KCNQ1OT1 at Imprinting centre 2 on … (more)

Functional evidence

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Functional consequence Method Result Submitter Supporting information
variation affecting protein function
  1. Method not provided
  2. Method not provided
  1. Result not provided
  2. Result not provided
Genetics and Molecular Pathology Laboratory,Hudson Institute of Medical Research
Accession: SCV000599436.1
Submitted: (Sep 12, 2017)
Evidence details

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs757460628...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021