rs397509393
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP2PP3_ModeratePP5_Moderate
The NM_001130823.3(DNMT1):c.1814G>C(p.Gly605Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. G605G) has been classified as Likely benign.
Frequency
Consequence
NM_001130823.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DNMT1 | NM_001130823.3 | c.1814G>C | p.Gly605Ala | missense_variant | 21/41 | ENST00000359526.9 | |
DNMT1 | NM_001318730.2 | c.1766G>C | p.Gly589Ala | missense_variant | 20/40 | ||
DNMT1 | NM_001379.4 | c.1766G>C | p.Gly589Ala | missense_variant | 20/40 | ||
DNMT1 | NM_001318731.2 | c.1451G>C | p.Gly484Ala | missense_variant | 21/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DNMT1 | ENST00000359526.9 | c.1814G>C | p.Gly605Ala | missense_variant | 21/41 | 1 | NM_001130823.3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 90
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Autosomal dominant cerebellar ataxia, deafness and narcolepsy Pathogenic:2
Likely pathogenic, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Jan 10, 2018 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | May 15, 2012 | - - |
Hereditary sensory neuropathy-deafness-dementia syndrome Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | Inherited Neuropathy Consortium Ii, University Of Miami | Jan 06, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at