NM_012275.3(IL36RN):c.245C>T (p.Pro82Leu) AND Generalized pustular psoriasis

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Dec 9, 2023
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:: RCV000907339.12

Allele description [Variation Report for NM_012275.3(IL36RN):c.245C>T (p.Pro82Leu)]

NM_012275.3(IL36RN):c.245C>T (p.Pro82Leu)

Gene:

IL36RN:interleukin 36 receptor antagonist [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q14.1

Genomic location:

Preferred name:

NM_012275.3(IL36RN):c.245C>T (p.Pro82Leu)

HGVS:

NC_000002.12:g.113062454C>T
NG_031864.1:g.8817C>T
NM_012275.3:c.245C>TMANE SELECT
NM_173170.1:c.245C>T
NP_036407.1:p.Pro82Leu
NP_775262.1:p.Pro82Leu
LRG_730t1:c.245C>T
LRG_730t2:c.245C>T
LRG_730:g.8817C>T
LRG_730p1:p.Pro82Leu
NC_000002.11:g.113820031C>T
NM_012275.2:c.245C>T

Protein change:

P82L

Links:

dbSNP: rs144182857

NCBI 1000 Genomes Browser:

rs144182857

Molecular consequence:

NM_012275.3:c.245C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_173170.1:c.245C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Generalized pustular psoriasis
Identifiers:: MONDO: MONDO:0100491; MedGen: C0343055

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001052036	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Dec 9, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001288881	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Apr 27, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001052036

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Dec 9, 2023)

germline

clinical testing

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

SCV001288881

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Apr 27, 2017)

germline

clinical testing

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

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

Mutation analysis of the IL36RN gene in Chinese patients with generalized pustular psoriasis with/without psoriasis vulgaris.

Li X, Chen M, Fu X, Zhang Q, Wang Z, Yu G, Yu Y, Qin P, Wu W, Pan F, Liu H, Zhang F.

J Dermatol Sci. 2014 Nov;76(2):132-8. doi: 10.1016/j.jdermsci.2014.08.007. Epub 2014 Aug 26.

PubMed [citation]

PMID:: 25212972

Details of each submission

From Invitae, SCV001052036.6

#	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, SCV001288881.1

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

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: Feb 20, 2024

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