NM_001127208.3(TET2):c.2188del (p.Thr730fs) AND Immunodeficiency 75

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jan 3, 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:: RCV003150599.2

Allele description [Variation Report for NM_001127208.3(TET2):c.2188del (p.Thr730fs)]

NM_001127208.3(TET2):c.2188del (p.Thr730fs)

Genes:

TET2-AS1:TET2 antisense RNA 1 [Gene - HGNC]
TET2:tet methylcytosine dioxygenase 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

4q24

Genomic location:

Preferred name:

NM_001127208.3(TET2):c.2188del (p.Thr730fs)

HGVS:

NC_000004.12:g.105236130del
NG_028191.1:g.95256del
NM_001127208.3:c.2188delMANE SELECT
NM_017628.4:c.2188del
NP_001120680.1:p.Thr730Hisfs
NP_001120680.1:p.Thr730fs
NP_060098.3:p.Thr730fs
LRG_626t1:c.2188del
LRG_626t2:c.2188del
LRG_626:g.95256del
LRG_626p2:p.Thr730fs
NC_000004.11:g.106157287del
NM_001127208.2:c.2188del
NM_001127208.2:c.2188delA

Protein change:

T730fs

Molecular consequence:

NM_001127208.3:c.2188del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_017628.4:c.2188del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:: Immunodeficiency 75
Synonyms:: IMMUNODEFICIENCY 75 WITH LYMPHOPROLIFERATION
Identifiers:: MONDO: MONDO:0030858; MedGen: C5436860; OMIM: 619126

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003837564	Diagnostic Genetics, Severance Hospital, Yonsei University College of Medicine	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 3, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003837564

Diagnostic Genetics, Severance Hospital, Yonsei University College of Medicine

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jan 3, 2023)

germline

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Diagnostic Genetics, Severance Hospital, Yonsei University College of Medicine, SCV003837564.1

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

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

Last Updated: May 26, 2024

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