NM_005535.3(IL12RB1):c.1058G>A (p.Gly353Glu) AND Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 18, 2021
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:: RCV002051449.2

Allele description

NM_005535.3(IL12RB1):c.1058G>A (p.Gly353Glu)

Gene:

IL12RB1:interleukin 12 receptor subunit beta 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.11

Genomic location:

Preferred name:

NM_005535.3(IL12RB1):c.1058G>A (p.Gly353Glu)

HGVS:

NC_000019.10:g.18069677C>T
NG_007366.2:g.34273G>A
NM_001290023.2:c.1058G>A
NM_001290024.1:c.1178G>A
NM_005535.3:c.1058G>AMANE SELECT
NP_001276952.1:p.Gly353Glu
NP_001276953.1:p.Gly393Glu
NP_005526.1:p.Gly353Glu
LRG_72:g.34273G>A
NC_000019.9:g.18180487C>T

Protein change:

G353E

Links:

dbSNP: rs111768826

NCBI 1000 Genomes Browser:

rs111768826

Molecular consequence:

NM_001290023.2:c.1058G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001290024.1:c.1178G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_005535.3:c.1058G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Mendelian susceptibility to mycobacterial diseases due to complete IL12RB1 deficiency
Synonyms:: IL12RB1 DEFICIENCY; Immunodeficiency 30
Identifiers:: MONDO: MONDO:0013955; MedGen: C4013949; Orphanet: 319552; OMIM: 614891

Recent activity

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Homo sapiens syntabulin (SYBU), transcript variant 1, mRNA
Homo sapiens syntabulin (SYBU), transcript variant 1, mRNA
gi|1890250863|ref|NM_001099744.2|

Nucleotide
AIP3 ABI3-interacting protein 3 [Arabidopsis thaliana]
AIP3 ABI3-interacting protein 3 [Arabidopsis thaliana]
Gene ID:837400

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002109553	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 18, 2021)	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

SCV002109553

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 18, 2021)

germline

clinical testing

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

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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 Invitae, SCV002109553.2

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

Description

This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 353 of the IL12RB1 protein (p.Gly353Glu). This variant is present in population databases (rs111768826, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with IL12RB1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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: Dec 24, 2023

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