Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Variant: NM_002185.5(IL7R):c.704C>G (p.Ser235Ter)

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA359431210

578174 (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: 2e52e733-0d8f-4b99-8abe-bd00be08fc6b

Approved on: 2024-01-17

Published on: 2024-01-17

HGVS expressions

NM_002185.5:c.704C>G

NM_002185.5(IL7R):c.704C>G (p.Ser235Ter)

NC_000005.10:g.35873646C>G

CM000667.2:g.35873646C>G

NC_000005.9:g.35873748C>G

CM000667.1:g.35873748C>G

NC_000005.8:g.35909505C>G

NG_009567.1:g.21758C>G

ENST00000303115.8:c.704C>G

ENST00000303115.7:c.704C>G

ENST00000505093.1:c.113C>G

ENST00000506850.5:c.704C>G

ENST00000509668.1:n.446C>G

ENST00000514217.5:c.538-1866C>G

NM_002185.3:c.704C>G

NR_120485.1:n.641-1866C>G

NM_002185.4:c.704C>G

NR_120485.2:n.667-1866C>G

NR_120485.3:n.625-1866C>G

Likely Pathogenic

PM2_Supporting PVS1

BS2

Evidence Links 0

Expert Panel

Severe Combined Immunodeficiency Disease VCEP

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

The c.704C>G (p.Ser235Ter)(NM_002185.5) variant in IL7R is a nonsense variant predicted to cause a premature stop codon in biologically-relevant-exon 5/8 leading to nonsense-mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). The variant has not been identified in the literature to our knowledge. In summary, this variant meets the criteria to be classified as likely pathogenic for SCID. ACMG/AMP criteria applied, as specified by the ClinGen SCID-VCEP: PVS1, PM2_Supporting. (VCEP specifications version 1).

PM2_Supporting

This variant is absent from gnomAD v2.1.1 (PM2_Supporting).

PVS1

BS2

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

Curation History

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