NM_000565.4(IL6R):c.1189C>G (p.Leu397Val) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 19, 2022
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:: RCV001982286.3

Allele description [Variation Report for NM_000565.4(IL6R):c.1189C>G (p.Leu397Val)]

NM_000565.4(IL6R):c.1189C>G (p.Leu397Val)

Gene:

IL6R:interleukin 6 receptor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q21.3

Genomic location:

Preferred name:

NM_000565.4(IL6R):c.1189C>G (p.Leu397Val)

HGVS:

NC_000001.11:g.154465162C>G
NG_012087.1:g.64970C>G
NM_000565.3:c.1189C>G
NM_000565.4:c.1189C>GMANE SELECT
NM_001382769.1:c.1288C>G
NM_001382770.1:c.1282C>G
NM_001382771.1:c.1237C>G
NM_001382772.1:c.1183C>G
NM_001382773.1:c.1143C>G
NM_001382774.1:c.829C>G
NM_181359.3:c.1095C>G
NP_000556.1:p.Leu397Val
NP_001369698.1:p.Leu430Val
NP_001369699.1:p.Leu428Val
NP_001369700.1:p.Leu413Val
NP_001369701.1:p.Leu395Val
NP_001369702.1:p.Leu381=
NP_001369703.1:p.Leu277Val
NP_852004.1:p.Leu365=
NC_000001.10:g.154437638C>G

Protein change:

L277V

Links:

dbSNP: rs137976773

NCBI 1000 Genomes Browser:

rs137976773

Molecular consequence:

NM_000565.4:c.1189C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382769.1:c.1288C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382770.1:c.1282C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382771.1:c.1237C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382772.1:c.1183C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382774.1:c.829C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382773.1:c.1143C>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_181359.3:c.1095C>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002211235	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 19, 2022)	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

SCV002211235

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 19, 2022)

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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002211235.2

#	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 leucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 397 of the IL6R protein (p.Leu397Val). This variant is present in population databases (rs137976773, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with IL6R-related conditions. ClinVar contains an entry for this variant (Variation ID: 1433555). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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: Nov 10, 2024

ClinVar

Relating variation to medicine