NC_000011.9:g.(?_117856768)_(118972385_?)dup AND Immunodeficiency 19

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 26, 2020
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:: RCV001322413.2

Allele description [Variation Report for NC_000011.9:g.(?_117856768)_(118972385_?)dup]

NC_000011.9:g.(?_117856768)_(118972385_?)dup

Genes:

ATP5MG:ATP synthase membrane subunit g [Gene - OMIM - HGNC]
BCL9L:BCL9 like [Gene - OMIM - HGNC]
CXCR5:C-X-C motif chemokine receptor 5 [Gene - OMIM - HGNC]
CD3D:CD3 delta subunit of T-cell receptor complex [Gene - OMIM - HGNC]
CD3E:CD3 epsilon subunit of T-cell receptor complex [Gene - OMIM - HGNC]
CD3G:CD3 gamma subunit of T-cell receptor complex [Gene - OMIM - HGNC]
DDX6:DEAD-box helicase 6 [Gene - OMIM - HGNC]
H2AX:H2A.X variant histone [Gene - OMIM - HGNC]
VPS11:VPS11 core subunit of CORVET and HOPS complexes [Gene - OMIM - HGNC]
ARCN1:archain 1 [Gene - OMIM - HGNC]
CENATAC:centrosomal AT-AC splicing factor [Gene - OMIM - HGNC]
DPAGT1:dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 [Gene - OMIM - HGNC]
FOXR1:forkhead box R1 [Gene - OMIM - HGNC]
HMBS:hydroxymethylbilane synthase [Gene - OMIM - HGNC]
HYOU1:hypoxia up-regulated 1 [Gene - OMIM - HGNC]
IL10RA:interleukin 10 receptor subunit alpha [Gene - OMIM - HGNC]
IFT46:intraflagellar transport 46 [Gene - OMIM - HGNC]
JAML:junction adhesion molecule like [Gene - OMIM - HGNC]
KMT2A:lysine methyltransferase 2A [Gene - OMIM - HGNC]
MPZL2:myelin protein zero like 2 [Gene - OMIM - HGNC]
MPZL3:myelin protein zero like 3 [Gene - OMIM - HGNC]
PHLDB1:pleckstrin homology like domain family B member 1 [Gene - OMIM - HGNC]
RPS25:ribosomal protein S25 [Gene - OMIM - HGNC]
SCN2B:sodium voltage-gated channel beta subunit 2 [Gene - OMIM - HGNC]
SCN4B:sodium voltage-gated channel beta subunit 4 [Gene - OMIM - HGNC]
SLC37A4:solute carrier family 37 member 4 [Gene - OMIM - HGNC]
TTC36:tetratricopeptide repeat domain 36 [Gene - OMIM - HGNC]
TRAPPC4:trafficking protein particle complex subunit 4 [Gene - OMIM - HGNC]
TMEM25:transmembrane protein 25 [Gene - OMIM - HGNC]
TMPRSS4:transmembrane serine protease 4 [Gene - OMIM - HGNC]
TREH:trehalase [Gene - OMIM - HGNC]
UBE4A:ubiquitination factor E4A [Gene - OMIM - HGNC]
UPK2:uroplakin 2 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

11q23.3

Genomic location:

Chr11: 117856768 - 118972385 (on Assembly GRCh37)

Preferred name:

NC_000011.9:g.(?_117856768)_(118972385_?)dup

HGVS:

NC_000011.9:g.(?_117856768)_(118972385_?)dup

Condition(s)

Name:: Immunodeficiency 19 (IMD19)
Synonyms:: CD3-DELTA DEFICIENCY; SEVERE COMBINED IMMUNODEFICIENCY, T CELL-NEGATIVE, B CELL-POSITIVE, NK CELL-POSITIVE; SCID, T CELL-NEGATIVE, B CELL-POSITIVE, NK CELL-POSITIVE; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0014280; MedGen: C3810147; OMIM: 615617

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001513281	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 26, 2020)	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

SCV001513281

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 26, 2020)

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001513281.1

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

Description

This variant results in a copy number gain of the genomic region encompassing the full coding sequence of the CD3D gene. The boundaries of this event are unknown as they extend beyond the assayed region for this gene and therefore may encompass additional genes. As the precise location of this event is unknown, it may be in tandem or it may be located elsewhere in the genome. This variant has not been reported in the literature in individuals with CD3D-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Jan 13, 2025

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