NM_002187.3(IL12B):c.364+1G>T AND Mendelian susceptibility to mycobacterial diseases due to complete IL12B deficiency

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Dec 15, 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:: RCV003586641.1

Allele description [Variation Report for NM_002187.3(IL12B):c.364+1G>T]

NM_002187.3(IL12B):c.364+1G>T

Gene:

IL12B:interleukin 12B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q33.3

Genomic location:

Preferred name:

NM_002187.3(IL12B):c.364+1G>T

HGVS:

NC_000005.10:g.159323053C>A
NG_009618.1:g.12421G>T
NM_002187.3:c.364+1G>TMANE SELECT
LRG_71:g.12421G>T
NC_000005.9:g.158750061C>A

Molecular consequence:

NM_002187.3:c.364+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Mendelian susceptibility to mycobacterial diseases due to complete IL12B deficiency
Synonyms:: IL12B DEFICIENCY; Immunodeficiency 29
Identifiers:: MONDO: MONDO:0013954; MedGen: C4013948; Orphanet: 319558; OMIM: 614890

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004250586	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Dec 15, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 16199547, 11753820, 23429356, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004250586

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Dec 15, 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

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

Inherited interleukin-12 deficiency: IL12B genotype and clinical phenotype of 13 patients from six kindreds.

Picard C, Fieschi C, Altare F, Al-Jumaah S, Al-Hajjar S, Feinberg J, Dupuis S, Soudais C, Al-Mohsen IZ, Génin E, Lammas D, Kumararatne DS, Leclerc T, Rafii A, Frayha H, Murugasu B, Wah LB, Sinniah R, Loubser M, Okamoto E, Al-Ghonaium A, Tufenkeji H, et al.

Am J Hum Genet. 2002 Feb;70(2):336-48. Epub 2001 Dec 17.

PubMed [citation]

PMID:: 11753820
PMCID:: PMC384913

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV004250586.1

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

Description

This sequence change affects a donor splice site in intron 3 of the IL12B gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in IL12B are known to be pathogenic (PMID: 11753820, 23429356). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with IL12B-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely 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: Feb 20, 2024

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