Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_002185.5(IL7R):c.355A>T (p.Lys119Ter)

CA359428593

642787 (ClinVar)

Gene: IL7R
Condition: severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: 0cbc2c97-0ef2-4c8f-baf6-f6fc26c5e7c5
Approved on: 2024-01-30
Published on: 2024-01-30

HGVS expressions

NM_002185.5:c.355A>T
NM_002185.5(IL7R):c.355A>T (p.Lys119Ter)
NC_000005.10:g.35867439A>T
CM000667.2:g.35867439A>T
NC_000005.9:g.35867541A>T
CM000667.1:g.35867541A>T
NC_000005.8:g.35903298A>T
NG_009567.1:g.15551A>T
ENST00000303115.8:c.355A>T
ENST00000303115.7:c.355A>T
ENST00000506850.5:c.355A>T
ENST00000511031.1:n.489A>T
ENST00000511982.1:c.355A>T
ENST00000514217.5:c.355A>T
NM_002185.3:c.355A>T
NR_120485.1:n.458A>T
NM_002185.4:c.355A>T
NR_120485.2:n.484A>T
NR_120485.3:n.442A>T

Likely Pathogenic

Met criteria codes 2
PM2_Supporting PVS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Severe Combined Immunodeficiency Disease Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for IL7R Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Severe Combined Immunodeficiency Disease VCEP
c.355A>T (p.Lys119Ter)(NM_002185.5) variant in IL7R is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 3/8 leading to nonsense-mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1_Met).The variant is absent in gnomAD v4 (PM2_supporting). There are no publications for this variant in the literature. As per the SCID VCEP specifications and the Bayesian interpretation of the ACMG/AMP combining rules, 1 very strong and 1 supporting criteria results in a Likely Pathogenic classification. In summary, this variant meets the criteria to be classified as Likely Pathogenic variant for autosomal recessive severe combined immunodeficiency due to IL7R deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP: PVS1_Met,PM2_supporting (VCEP specifications version 1).
Met criteria codes
PM2_Supporting
The variant is absent in gnomAD v4 (PM2_supporting).
PVS1
c.355A>T (p.Lys119Ter)(NM_002185.5) variant in IL7R is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 3/8 leading to nonsense-mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1 Met).
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