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NM_002185.5(IL7R):c.214G>C (p.Glu72Gln) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 19, 2019
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:
RCV000030059.2

Allele description [Variation Report for NM_002185.5(IL7R):c.214G>C (p.Glu72Gln)]

NM_002185.5(IL7R):c.214G>C (p.Glu72Gln)

Gene:
IL7R:interleukin 7 receptor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5p13.2
Genomic location:
Preferred name:
NM_002185.5(IL7R):c.214G>C (p.Glu72Gln)
HGVS:
  • NC_000005.10:g.35860983G>C
  • NG_009567.1:g.9095G>C
  • NM_002185.5:c.214G>CMANE SELECT
  • NP_002176.2:p.Glu72Gln
  • LRG_74t1:c.214G>C
  • LRG_74:g.9095G>C
  • NC_000005.9:g.35861085G>C
  • NM_002185.2:c.214G>C
  • NM_002185.3:c.214G>C
  • NR_120485.3:n.301G>C
Protein change:
E72Q
Links:
dbSNP: rs148001159
NCBI 1000 Genomes Browser:
rs148001159
Molecular consequence:
  • NM_002185.5:c.214G>C - missense variant - [Sequence Ontology: SO:0001583]
  • NR_120485.3:n.301G>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000052714Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Uncertain significance
(Nov 19, 2019) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000052714.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: IL7R c.214G>C (p.Glu72Gln) results in a conservative amino acid change located in the IL-7Ralpha, fibronectin type III domain (IPR040997) of the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00024 in 251020 control chromosomes (gnomAD). This frequency is not significantly higher than expected for a pathogenic variant in IL7R causing Severe Combined Immunodeficiency Syndrome (0.00024 vs 0.0013), allowing no conclusion about variant significance. To our knowledge, no occurrence of c.214G>C in individuals affected with Severe Combined Immunodeficiency Syndrome and no experimental evidence demonstrating an impact on protein function have been reported. Two other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Both laboratories cited the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024