NC_000006.11:g.(?_137143759)_(138202456_?)del AND not provided

This record was updated by the submitter. Please see the current version.

Germline classification:: no classifications from unflagged records (1 submission)
Review status:: no classifications from unflagged records

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:: RCV002004826.6

Allele description

NC_000006.11:g.(?_137143759)_(138202456_?)del

Genes:

TNFAIP3:TNF alpha induced protein 3 [Gene - OMIM - HGNC]
IFNGR1:interferon gamma receptor 1 [Gene - OMIM - HGNC]
IL20RA:interleukin 20 receptor subunit alpha [Gene - OMIM - HGNC]
IL22RA2:interleukin 22 receptor subunit alpha 2 [Gene - OMIM - HGNC]
LINC02539:long intergenic non-protein coding RNA 2539 [Gene - HGNC]
OLIG3:oligodendrocyte transcription factor 3 [Gene - OMIM - HGNC]
PEX7:peroxisomal biogenesis factor 7 [Gene - OMIM - HGNC]
SLC35D3:solute carrier family 35 member D3 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

6q23.3

Genomic location:

Chr6: 137143759 - 138202456 (on Assembly GRCh37)

Preferred name:

NC_000006.11:g.(?_137143759)_(138202456_?)del

HGVS:

NC_000006.11:g.(?_137143759)_(138202456_?)del

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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No clinical assertions found. See "Flagged submissions" below.

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Summary from all submissions

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

Citations

PubMed

Loss-of-function mutations in TNFAIP3 leading to A20 haploinsufficiency cause an early-onset autoinflammatory disease.

Zhou Q, Wang H, Schwartz DM, Stoffels M, Park YH, Zhang Y, Yang D, Demirkaya E, Takeuchi M, Tsai WL, Lyons JJ, Yu X, Ouyang C, Chen C, Chin DT, Zaal K, Chandrasekharappa SC, Hanson EP, Yu Z, Mullikin JC, Hasni SA, Wertz IE, et al.

Nat Genet. 2016 Jan;48(1):67-73. doi: 10.1038/ng.3459. Epub 2015 Dec 7.

PubMed [citation]

PMID:: 26642243
PMCID:: PMC4777523

TNFAIP3 haploinsufficiency is the cause of autoinflammatory manifestations in a patient with a deletion of 13Mb on chromosome 6.

Franco-Jarava C, Wang H, Martin-Nalda A, Alvarez SD, García-Prat M, Bodet D, García-Patos V, Plaja A, Rudilla F, Rodriguez-Sureda V, García-Latorre L, Aksentijevich I, Colobran R, Soler-Palacín P.

Clin Immunol. 2018 Jun;191:44-51. doi: 10.1016/j.clim.2018.03.009. Epub 2018 Mar 20.

PubMed [citation]

PMID:: 29572183

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV002232003.3

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

Description

A gross deletion of the genomic region encompassing the full coding sequence of the TNFAIP3 gene has been identified. Loss-of-function variants in TNFAIP3 are known to be pathogenic (PMID: 26642243). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. Isolated whole-gene deletions of TNFAIP3 have not been reported in the literature. However, larger copy number events that include this gene have been reported (PMID: 29572183). For these reasons, this variant has been classified as Pathogenic.

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

Flagged submissions

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002232003	Invitae	flagged submission Reason: This record appears to be redundant with a more recent record from the same submitter. Notes: SCV002232003 appears to be redundant with SCV002242918. (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 23, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 26642243, 29572183, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002232003

Invitae

flagged submission

Reason: This record appears to be redundant with a more recent record from the same submitter.

Notes: SCV002232003 appears to be redundant with SCV002242918.

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 23, 2022)

germline

clinical testing

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

Last Updated: Jun 9, 2024

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