NM_002187.3(IL12B):c.97G>A (p.Val33Ile) AND Mendelian susceptibility to mycobacterial diseases due to complete IL12B deficiency

Germline classification:: Benign (2 submissions)
Last evaluated:: Jan 31, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000545923.15

Allele description [Variation Report for NM_002187.3(IL12B):c.97G>A (p.Val33Ile)]

NM_002187.3(IL12B):c.97G>A (p.Val33Ile)

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.97G>A (p.Val33Ile)

HGVS:

NC_000005.10:g.159323321C>T
NG_009618.1:g.12153G>A
NM_002187.3:c.97G>AMANE SELECT
NP_002178.2:p.Val33Ile
NP_002178.2:p.Val33Ile
LRG_71t1:c.97G>A
LRG_71:g.12153G>A
LRG_71p1:p.Val33Ile
NC_000005.9:g.158750329C>T
NM_002187.2:c.97G>A

Protein change:

V33I

Links:

dbSNP: rs3213096

NCBI 1000 Genomes Browser:

rs3213096

Molecular consequence:

NM_002187.3:c.97G>A - missense variant - [Sequence Ontology: SO:0001583]

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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LOC109840503 [Asparagus officinalis]
Gene ID:109840503

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000655060	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 31, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001317155	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Apr 27, 2017)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 18449199, 17236132 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000655060

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Jan 31, 2024)

germline

clinical testing

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

SCV001317155

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Apr 27, 2017)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

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

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

IL12B polymorphisms are linked but not associated with Plasmodium falciparum parasitemia: a familial study in Burkina Faso.

Barbier M, Atkinson A, Fumoux F, Rihet P.

Genes Immun. 2008 Jul;9(5):405-11. doi: 10.1038/gene.2008.31. Epub 2008 May 1.

PubMed [citation]

PMID:: 18449199

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000655060.8

#	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

From Illumina Laboratory Services, Illumina, SCV001317155.1

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

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.

#	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: Oct 20, 2024

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