NM_000206.3(IL2RG):c.318A>G (p.Leu106=) AND X-linked severe combined immunodeficiency

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

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: May 30, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV001563867.5

Allele description

NM_000206.3(IL2RG):c.318A>G (p.Leu106=)

Gene:

IL2RG:interleukin 2 receptor subunit gamma [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

Xq13.1

Genomic location:

Preferred name:

NM_000206.3(IL2RG):c.318A>G (p.Leu106=)

HGVS:

NC_000023.11:g.71110640T>C
NG_009088.1:g.5914A>G
NG_021141.1:g.1149A>G
NM_000206.3:c.318A>GMANE SELECT
NP_000197.1:p.Leu106=
LRG_150:g.5914A>G
NC_000023.10:g.70330490T>C

Links:

dbSNP: rs1389116834

NCBI 1000 Genomes Browser:

rs1389116834

Molecular consequence:

NM_000206.3:c.318A>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: X-linked severe combined immunodeficiency (SCIDX1)
Synonyms:: IMMUNODEFICIENCY 4; X-Linked Combined Immunodeficiency Diseases; Severe combined immunodeficiency, X-linked, T cell-negative, B cell-positive, NK cell-negative; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0010315; MedGen: C1279481; Orphanet: 276; OMIM: 300400

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PREDICTED: Homo sapiens GREB1 like retinoic acid receptor coactivator (GREB1L), ...
PREDICTED: Homo sapiens GREB1 like retinoic acid receptor coactivator (GREB1L), transcript variant X10, mRNA
gi|2217317681|ref|XM_047437814.1|

Nucleotide
602509062F1 NIH_MGC_79 Homo sapiens cDNA clone IMAGE:4619679 5', mRNA sequence
602509062F1 NIH_MGC_79 Homo sapiens cDNA clone IMAGE:4619679 5', mRNA sequence
gi|13342906|gnl|dbEST|8124494|gb|BG 0.1|

Nucleotide
GREB1-like protein isoform X12 [Homo sapiens]
GREB1-like protein isoform X12 [Homo sapiens]
gi|2462561524|ref|XP_054175116.1|

Protein
GREB1-like protein isoform X1 [Homo sapiens]
GREB1-like protein isoform X1 [Homo sapiens]
gi|2217317667|ref|XP_047293765.1|

Protein
Mouse ribosomal protein L7 (rpL7) gene, complete cds
Mouse ribosomal protein L7 (rpL7) gene, complete cds
gi|200784|gb|M29015.1|MUSRPL7A

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001786914	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Jul 14, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003298475	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (May 30, 2023)	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

SCV001786914

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Jul 14, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV003298475

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(May 30, 2023)

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
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

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 Genome-Nilou Lab, SCV001786914.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Invitae, SCV003298475.2

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

#	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: Feb 28, 2024

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