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.361dup (p.Ile121fs)

CA357950

224841 (ClinVar)

Gene: IL7R
Condition: severe combined immunodeficiency, autosomal recessive, T cell-negative, B cell-positive, NK cell-positive
Inheritance Mode: Autosomal recessive inheritance
UUID: c0cf220b-a662-4fb9-b379-a971a97367b5

HGVS expressions

NM_002185.5:c.361dup
NM_002185.5(IL7R):c.361dup (p.Ile121fs)
NC_000005.10:g.35867445dup
CM000667.2:g.35867445dup
NC_000005.9:g.35867547dup
CM000667.1:g.35867547dup
NC_000005.8:g.35903304dup
NG_009567.1:g.15557dup
ENST00000303115.8:c.361dup
ENST00000303115.7:c.361dup
ENST00000506850.5:c.361dup
ENST00000511031.1:n.495dup
ENST00000511982.1:c.361dup
ENST00000514217.5:c.361dup
NM_002185.3:c.361dup
NR_120485.1:n.464dup
NM_002185.4:c.361dup
NR_120485.2:n.490dup
NR_120485.3:n.448dup

Pathogenic

Met criteria codes 3
PVS1 PP4 PM2_Supporting
Not Met criteria codes 1
BS2

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
The NM_002185.5(IL7R):c.361dup (p.Ile121AsnfsTer8) frameshift variant in exon 3 creates a premature stop codon in exon 4/5 (upstream of the final 50 nucleotides), which is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). This variant has been reported in several SCID patients (PMIDs: 35503492, 24759676, 32765500, 28436970, 25046553), at least one of whom was reported with a highly specific phenotype; the diagnosis of SCID was made by criteria of the Primary Immune Deficiency Treatment Consortium in this patient with a T−BlowNK+ (0 CD3+ cells/mm, 300 B cells/mm3, 450 NK cells/mm3) lymphocyte subset profile (PMID: 35503492; PP4). The filtering allele frequency based on the European (non-Finnish) population (upper bound of 95% CI of 9/128422 observed alleles) is 0.00002867 in gnomAD v2.1.1 which is below the SCID-VCEP threshold (<0.00004129) and therefore meets this criterion (PM2_Supporting). In summary, this variant meets the criteria to be classified as Pathogenic for autosomal recessive SCID based on the ACMG/AMP criteria applied, as specified by the ClinGen SCID VCEP. Criteria applied: PVS1, PM2_supporting, PP4. (VCEP specifications version 1).
Met criteria codes
PVS1
The NM_002185.5(IL7R):c.361dup (p.Ile121AsnfsTer8) frameshift variant in exon 3 creates a premature stop codon in exon 4/5 (upstream of the final 50 nucleotides), which is predicted to lead to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1).
PP4
At least one patient with this variant, identified through WES, is reported with a highly specific phenotype; the diagnosis of SCID was made by criteria of the Primary Immune Deficiency Treatment Consortium in this patient with a T−BlowNK+ (0 CD3+ cells/mm, 300 B cells/mm3, 450 NK cells/mm3) lymphocyte subset profile (PMID: 35503492; PP4).
PM2_Supporting
The filtering allele frequency based on the European (non-Finnish) population (upper bound of 95% CI of 9/128422 observed alleles) is 0.00002867 in gnomAD v2.1.1 which is below the SCID-VCEP threshold (<0.00004129) and therefore meets this criterion (PM2_Supporting).
Not Met criteria codes
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2024-01-17
Published on: 2024-01-17
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