NC_000005.10:g.(?_35860832)_(35871233_?)del AND Immunodeficiency 104

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 1, 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:: RCV000805916.9

Allele description [Variation Report for NC_000005.10:g.(?_35860832)_(35871233_?)del]

NC_000005.10:g.(?_35860832)_(35871233_?)del

Genes:

LOC129993794:ATAC-STARR-seq lymphoblastoid active region 22471 [Gene]
IL7R:interleukin 7 receptor [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

5p13.2

Genomic location:

Preferred name:

NC_000005.10:g.(?_35860832)_(35871233_?)del

HGVS:

NC_000005.10:g.(?_35860832)_(35871233_?)del
NC_000005.9:g.(?_35860934)_(35871335_?)del

Condition(s)

Name:: Immunodeficiency 104
Synonyms:: SCID, AUTOSOMAL RECESSIVE, T CELL-NEGATIVE, B CELL-POSITIVE, NK CELL-POSITIVE; Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive; IMMUNODEFICIENCY 104, SEVERE COMBINED; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0012163; MedGen: C5676890; OMIM: 608971

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000945891	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 1, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 21664875, 26123418, 27807805, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000945891

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 1, 2023)

germline

clinical testing

PubMed (4)
[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

Clinical and immunological manifestations of patients with atypical severe combined immunodeficiency.

Felgentreff K, Perez-Becker R, Speckmann C, Schwarz K, Kalwak K, Markelj G, Avcin T, Qasim W, Davies EG, Niehues T, Ehl S.

Clin Immunol. 2011 Oct;141(1):73-82. doi: 10.1016/j.clim.2011.05.007. Epub 2011 May 30. Review.

PubMed [citation]

PMID:: 21664875

Hypomorphic interleukin-7 receptor α-chain mutations and T-cell deficiency: a delay in diagnosis.

Leiding JW, Sriaroon P, Ly JM, Petrovic A, Howard DL, Shamblott M, Kuehn HS, Fleisher TA.

Ann Allergy Asthma Immunol. 2015 Jul;115(1):1-3. doi: 10.1016/j.anai.2015.04.024. No abstract available.

PubMed [citation]

PMID:: 26123418

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000945891.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 2-4 of the IL7R gene. This deletion is out-of-frame, and is expected to create a premature termination codon and result in an absent or disrupted protein product. Loss-of-function variants in IL7R are known to be pathogenic (PMID: 21664875, 26123418). A similar copy number variant has been observed in individual(s) with T-B+NK+ severe combined immunodeficiency (PMID: 27807805). 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

Last Updated: Sep 29, 2024

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