NC_000020.10:g.(?_43248920)_(43264949_?)del AND Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-negative, due to adenosine deaminase deficiency

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 9, 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:: RCV004579454.2

Allele description [Variation Report for NC_000020.10:g.(?_43248920)_(43264949_?)del]

NC_000020.10:g.(?_43248920)_(43264949_?)del

Gene:: ADA:adenosine deaminase [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 20q13.12
Genomic location:: Chr20: 43248920 - 43264949 (on Assembly GRCh37)
Preferred name:: NC_000020.10:g.(?_43248920)_(43264949_?)del
HGVS:: NC_000020.10:g.(?_43248920)_(43264949_?)del
This HGVS expression did not pass validation

Condition(s)

Name:: Severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-negative, NK cell-negative, due to adenosine deaminase deficiency
Synonyms:: ADA-SCID; SCID DUE TO ADA DEFICIENCY, EARLY-ONSET; ADA deficiency; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0007064; MedGen: C1863236; Orphanet: 277; OMIM: 102700

Recent activity

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Vegetative stage ( 4 pairs of true leaves) female apical meristem RNA-seq biolog...
Vegetative stage ( 4 pairs of true leaves) female apical meristem RNA-seq biological repeat 4

biosample
MAG: 30S ribosomal protein S6 [Clostridium sp. CAG:354_28_25]
MAG: 30S ribosomal protein S6 [Clostridium sp. CAG:354_28_25]
gi|1124992461|gb|OKZ61053.1||gnl|WG L|BHV96_00220

Protein
MAG: formate C-acetyltransferase [Clostridium sp. CAG:354_28_25]
MAG: formate C-acetyltransferase [Clostridium sp. CAG:354_28_25]
gi|1124992458|gb|OKZ61050.1||gnl|WG L|BHV96_00205

Protein
MAG: hypothetical protein BHV96_00255 [Clostridium sp. CAG:354_28_25]
MAG: hypothetical protein BHV96_00255 [Clostridium sp. CAG:354_28_25]
gi|1124992468|gb|OKZ61060.1||gnl|WG L|BHV96_00255

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV005063455	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 9, 2023)	unknown	clinical testing	PubMed (2) [See all records that cite these PMIDs] 8227344, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005063455

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 9, 2023)

unknown

clinical testing

PubMed (2)
[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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Novel splicing, missense, and deletion mutations in seven adenosine deaminase-deficient patients with late/delayed onset of combined immunodeficiency disease. Contribution of genotype to phenotype.

Santisteban I, Arredondo-Vega FX, Kelly S, Mary A, Fischer A, Hummell DS, Lawton A, Sorensen RU, Stiehm ER, Uribe L, et al.

J Clin Invest. 1993 Nov;92(5):2291-302.

PubMed [citation]

PMID:: 8227344
PMCID:: PMC288410

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, SCV005063455.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 2-11 of the ADA gene. While this deletion is not anticipated to lead to nonsense mediated decay, it is expected to disrupt the C-terminus of the protein. For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the ADA protein in which other variant(s) (p.Arg341Glyfs*8) have been determined to be pathogenic (PMID: 8227344; Invitae). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. This variant has not been reported in the literature in individuals affected with ADA-related conditions.

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

Last Updated: Sep 29, 2024

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