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NM_001287491.2(TET3):c.1215del (p.Trp406fs) AND Beck-Fahrner syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 16, 2020
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV001007573.3

Allele description [Variation Report for NM_001287491.2(TET3):c.1215del (p.Trp406fs)]

NM_001287491.2(TET3):c.1215del (p.Trp406fs)

Gene:
TET3:tet methylcytosine dioxygenase 3 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
2p13.1
Genomic location:
Preferred name:
NM_001287491.2(TET3):c.1215del (p.Trp406fs)
HGVS:
  • NC_000002.12:g.74047132del
  • NM_001287491.2:c.1215delMANE SELECT
  • NM_001366022.1:c.936del
  • NP_001274420.1:p.Trp406fs
  • NP_001352951.1:p.Trp313fs
  • NC_000002.11:g.74274259del
  • NM_001287491.1:c.1215delA
Protein change:
W313fs
Links:
OMIM: 613555.0009; dbSNP: rs1573779765
NCBI 1000 Genomes Browser:
rs1573779765
Molecular consequence:
  • NM_001287491.2:c.1215del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001366022.1:c.936del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Beck-Fahrner syndrome (BEFAHRS)
Identifiers:
MONDO: MONDO:0032922; MedGen: C5394097; OMIM: 618798

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001167194OMIM
no assertion criteria provided
Pathogenic
(Jun 16, 2020) 		germlineliterature only

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

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

Details of each submission

From OMIM, SCV001167194.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

In a 10-year-old boy of Ashkenazi Jewish descent (family 8) with autosomal dominant Beck-Fahrner syndrome (BEFAHRS; 618798), Beck et al. (2020) identified a de novo heterozygous 1-bp deletion (c.1215delA, NM_001287491.1) in the TET3 gene, predicted to result in a frameshift and premature termination (Trp406GlyfsTer135). The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not found in the gnomAD database. Functional studies of the variant and studies of patient cells were not performed, but it was predicted to result in haploinsufficiency.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jan 7, 2023