NC_000006.11:g.(?_137143759)_(138202456_?)del AND Disseminated atypical mycobacterial infection

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 23, 2022
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:: RCV002014736.6

Allele description [Variation Report for NC_000006.11:g.(?_137143759)_(138202456_?)del]

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)

Name:: Disseminated atypical mycobacterial infection
Identifiers:: MedGen: C0694566

Recent activity

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DNA-directed RNA polymerase subunit beta' [Stappia sp. WLB 29]
DNA-directed RNA polymerase subunit beta' [Stappia sp. WLB 29]
gi|2241394620|ref|WP_249696608.1|

Protein
50S ribosomal protein L11 [Stappia sp. WLB 29]
50S ribosomal protein L11 [Stappia sp. WLB 29]
gi|2241394627|ref|WP_249696615.1|

Protein
DNA-directed RNA polymerase subunit beta [Stappia sp. WLB 29]
DNA-directed RNA polymerase subunit beta [Stappia sp. WLB 29]
gi|2241394621|ref|WP_249696609.1|

Protein
PREDICTED: Rattus norvegicus eukaryotic translation initiation factor 3, subunit...
PREDICTED: Rattus norvegicus eukaryotic translation initiation factor 3, subunit D (Eif3d), transcript variant X1, mRNA
gi|2678958852|ref|XM_006241938.5|

Nucleotide
Arthrobacter sp. ok909 genome assembly, contig: Ga0066717_113, whole genome shot...
Arthrobacter sp. ok909 genome assembly, contig: Ga0066717_113, whole genome shotgun sequence
gi|1086930489|emb|FNJS01000013.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002242918	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 23, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 8960473, 9806040, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002242918

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 23, 2022)

germline

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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A mutation in the interferon-gamma-receptor gene and susceptibility to mycobacterial infection.

Newport MJ, Huxley CM, Huston S, Hawrylowicz CM, Oostra BA, Williamson R, Levin M.

N Engl J Med. 1996 Dec 26;335(26):1941-9.

PubMed [citation]

PMID:: 8960473

Abnormal regulation of interferon-gamma, interleukin-12, and tumor necrosis factor-alpha in human interferon-gamma receptor 1 deficiency.

Holland SM, Dorman SE, Kwon A, Pitha-Rowe IF, Frucht DM, Gerstberger SM, Noel GJ, Vesterhus P, Brown MR, Fleisher TA.

J Infect Dis. 1998 Oct;178(4):1095-104.

PubMed [citation]

PMID:: 9806040

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002242918.4

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

Description

This variant has not been reported in the literature in individuals affected with IFNGR1-related conditions. For these reasons, this variant has been classified as Pathogenic. A gross deletion of the genomic region encompassing the full coding sequence of the IFNGR1 gene has been identified. Loss-of-function variants in IFNGR1 are known to be pathogenic (PMID: 8960473, 9806040). The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes.

#	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

Last Updated: Sep 29, 2024

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