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NM_001130823.3(DNMT1):c.3524-16G>A AND Hereditary sensory neuropathy-deafness-dementia syndrome

Germline classification:
Likely benign (1 submission)
Last evaluated:
Oct 12, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV002063196.6

Allele description [Variation Report for NM_001130823.3(DNMT1):c.3524-16G>A]

NM_001130823.3(DNMT1):c.3524-16G>A

Gene:
DNMT1:DNA methyltransferase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.2
Genomic location:
Preferred name:
NM_001130823.3(DNMT1):c.3524-16G>A
HGVS:
  • NC_000019.10:g.10140344C>T
  • NG_028016.3:g.95943G>A
  • NM_001130823.3:c.3524-16G>AMANE SELECT
  • NM_001318730.2:c.3476-16G>A
  • NM_001318731.2:c.3161-16G>A
  • NM_001379.4:c.3476-16G>A
  • LRG_362t1:c.3524-16G>A
  • LRG_362:g.95943G>A
  • NC_000019.9:g.10251020C>T
  • NM_001130823.1:c.3524-16G>A
Links:
dbSNP: rs199694630
NCBI 1000 Genomes Browser:
rs199694630
Molecular consequence:
  • NM_001130823.3:c.3524-16G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001318730.2:c.3476-16G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001318731.2:c.3161-16G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001379.4:c.3476-16G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Hereditary sensory neuropathy-deafness-dementia syndrome
Synonyms:
HSN IE; NEUROPATHY, HEREDITARY SENSORY, WITH HEARING LOSS AND DEMENTIA; Hereditary sensory neuropathy type IE
Identifiers:
MONDO: MONDO:0013584; MedGen: C3279885; Orphanet: 456318; OMIM: 614116

Recent activity

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    Danio rerio raftlin family member 2, mRNA (cDNA clone MGC:56544 IMAGE:5914326), complete cds
    gi|30186163|gb|BC051615.1|
    Nucleotide
  • Bovinae tRNA-Phe, 12S ribosomal RNA, tRNA-Val, 16S ribosomal RNA, and tRNA-Leu g...
    Bovinae tRNA-Phe, 12S ribosomal RNA, tRNA-Val, 16S ribosomal RNA, and tRNA-Leu genes, complete sequence; NADH dehydrogenase subunit 1 (ND1) gene, complete cds; tRNA-Ile, tRNA-Gln, and tRNA-Met genes, complete sequence; NADH dehydrogenase subunit 2 (ND2) gene, complete cds; tRNA-Trp, tRNA-Ala, tRNA-Asn, tRNA-Cys, and tRNA-Tyr genes, complete sequence; cytochrome c oxidase subunit I (COX1) gene, complete cds; tRNA-Ser and tRNA-Asp genes, complete sequence; cytochrome c oxidase subunit II (COX2) gene, complete cds; tRNA-Lys gene, complete sequence; ATP synthase F0 subunit 8 (ATP8), ATP synthase F0 subunit 6 (ATP6), and cytochrome c oxidase subunit III (COX3) genes, complete cds; tRNA-Gly gene, complete sequence; NADH dehydrogenase subunit 3 (ND3) gene, complete cds; tRNA-Arg gene, complete sequence; NADH dehydrogenase subunit 4L (ND4L) and NADH dehydrogenase subunit 4 (ND4) genes, complete cds; tRNA-His, tRNA-Ser, and tRNA-Leu genes, complete sequence; NADH dehydrogenase subunit 5 (ND5) and NADH dehydrogenase subunit 6 (ND6) genes, complete cds; tRNA-Glu gene, complete sequence; cytochrome b (CYTB) gene, complete cds; and tRNA-Thr and tRNA-Pro genes, complete sequence; mitochondrial.
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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002449765Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely benign
(Oct 12, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002449765.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024