rs587776729
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PM4PP5
The NM_000206.3(IL2RG):c.711_712insCAGCATTGG(p.Gln235_Trp237dup) variant causes a inframe insertion change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 23)
Consequence
IL2RG
NM_000206.3 inframe_insertion
NM_000206.3 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.30
Genes affected
IL2RG (HGNC:6010): (interleukin 2 receptor subunit gamma) The protein encoded by this gene is an important signaling component of many interleukin receptors, including those of interleukin -2, -4, -7 and -21, and is thus referred to as the common gamma chain. Mutations in this gene cause X-linked severe combined immunodeficiency (XSCID), as well as X-linked combined immunodeficiency (XCID), a less severe immunodeficiency disorder. [provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
PM1
In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 3 uncertain in NM_000206.3
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_000206.3.
PP5
Variant X-71109273-T-TCCAATGCTG is Pathogenic according to our data. Variant chrX-71109273-T-TCCAATGCTG is described in ClinVar as [Pathogenic]. Clinvar id is 10024.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| IL2RG | NM_000206.3 | c.711_712insCAGCATTGG | p.Gln235_Trp237dup | inframe_insertion | 5/8 | ENST00000374202.7 | |
| IL2RG | XM_047442089.1 | c.711_712insCAGCATTGG | p.Gln235_Trp237dup | inframe_insertion | 5/7 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| IL2RG | ENST00000374202.7 | c.711_712insCAGCATTGG | p.Gln235_Trp237dup | inframe_insertion | 5/8 | 1 | NM_000206.3 | P1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
23
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome
GnomAD4 genome
Cov.:
23
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
X-linked severe combined immunodeficiency Pathogenic:1
| Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 1995 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at