NC_000002.11:g.(?_74307117)_(74307868_?)del AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jul 18, 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:: RCV004583768.2

Allele description [Variation Report for NC_000002.11:g.(?_74307117)_(74307868_?)del]

NC_000002.11:g.(?_74307117)_(74307868_?)del

Gene:: TET3:tet methylcytosine dioxygenase 3 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 2p13.1
Genomic location:: Chr2: 74307117 - 74307868 (on Assembly GRCh37)
Preferred name:: NC_000002.11:g.(?_74307117)_(74307868_?)del
HGVS:: NC_000002.11:g.(?_74307117)_(74307868_?)del
This HGVS expression did not pass validation

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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hypothetical protein [Streptococcus pyogenes]
hypothetical protein [Streptococcus pyogenes]
gi|499367174|ref|WP_011054752.1|

Protein
MULTISPECIES: adenylate kinase [Bacillus]
MULTISPECIES: adenylate kinase [Bacillus]
gi|489334752|ref|WP_003241987.1|

Protein
polysaccharide deacetylase family sporulation protein PdaB [Bacillus inaquosorum...
polysaccharide deacetylase family sporulation protein PdaB [Bacillus inaquosorum]
gi|489334716|ref|WP_003241951.1|

Protein
class I SAM-dependent methyltransferase [Bacillus inaquosorum]
class I SAM-dependent methyltransferase [Bacillus inaquosorum]
gi|489334727|ref|WP_003241962.1|

Protein
Receptor L-domain domain-containing protein [Caenorhabditis elegans]
Receptor L-domain domain-containing protein [Caenorhabditis elegans]
gi|1143472587|ref|NP_001335503.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005063393	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jul 18, 2023)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 34750377, 31928709, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005063393

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jul 18, 2023)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Deficiency of TET3 leads to a genome-wide DNA hypermethylation episignature in human whole blood.

Levy MA, Beck DB, Metcalfe K, Douzgou S, Sithambaram S, Cottrell T, Ansar M, Kerkhof J, Mignot C, Nougues MC, Keren B, Moore HW, Oegema R, Giltay JC, Simon M, van Jaarsveld RH, Bos J, van Haelst M, Motazacker MM, Boon EMJ, Santen GWE, Ruivenkamp CAL, et al.

NPJ Genom Med. 2021 Nov 8;6(1):92. doi: 10.1038/s41525-021-00256-y. Erratum in: NPJ Genom Med. 2021 Nov 24;6(1):100. doi: 10.1038/s41525-021-00269-7.

PubMed [citation]

PMID:: 34750377
PMCID:: PMC8576018

Delineation of a Human Mendelian Disorder of the DNA Demethylation Machinery: TET3 Deficiency.

Beck DB, Petracovici A, He C, Moore HW, Louie RJ, Ansar M, Douzgou S, Sithambaram S, Cottrell T, Santos-Cortez RLP, Prijoles EJ, Bend R, Keren B, Mignot C, Nougues MC, Õunap K, Reimand T, Pajusalu S, Zahid M, Saqib MAN, Buratti J, Seaby EG, et al.

Am J Hum Genet. 2020 Feb 6;106(2):234-245. doi: 10.1016/j.ajhg.2019.12.007. Epub 2020 Jan 9.

PubMed [citation]

PMID:: 31928709
PMCID:: PMC7010978

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV005063393.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with TET3-related conditions. This variant is a gross deletion of the genomic region encompassing exon(s) 5 of the TET3 gene. This deletion is out-of-frame, and is expected to create a premature termination codon and result in an absent or disrupted protein product. Loss-of-function variants in TET3 are known to be pathogenic (PMID: 34750377, 31928709).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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