X-71110633-C-G

Variant names:

• chrX-71110633-C-G
• rs17875899
• NM_000206.3:c.325G>C

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 4P and 2B. PM1 PM2 BP4_Moderate

The NM_000206.3(IL2RG):​c.325G>C​(p.Glu109Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E109K) has been classified as Benign.

• Frequency: Genomes: not found (cov: 22)
• Consequence: IL2RG NM_000206.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 6 publications found

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]

IL2RG Gene-Disease associations (from GenCC):

• T-B+ severe combined immunodeficiency due to gamma chain deficiency

  Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Orphanet, Ambry Genetics, Myriad Women’s Health
• Omenn syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000285171 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM1: In a hotspot region, there are 7 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 4 benign, 1 uncertain in NM_000206.3
• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.07621625).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000206.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL2RG	NM_000206.3	MANE Select	c.325G>C	p.Glu109Gln	missense	Exon 3 of 8	NP_000197.1
	IL2RG	NM_001438870.1		c.325G>C	p.Glu109Gln	missense	Exon 3 of 7	NP_001425799.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IL2RG	ENST00000374202.7	TSL:1 MANE Select	c.325G>C	p.Glu109Gln	missense	Exon 3 of 8	ENSP00000363318.3
	ENSG00000285171	ENST00000646505.1		n.325G>C		non_coding_transcript_exon	Exon 3 of 12	ENSP00000496673.1
	IL2RG	ENST00000482750.6	TSL:5	c.325G>C	p.Glu109Gln	missense	Exon 3 of 7	ENSP00000421262.2

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 22

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.095
BayesDel_addAF	Benign	-0.094	T
BayesDel_noAF	Benign	-0.37
CADD	Benign	4.8
DANN	Benign	0.57
DEOGEN2	Uncertain	0.47	T
FATHMM_MKL	Benign	0.077	N
LIST_S2	Benign	0.75	T
M_CAP	Benign	0.081	D
MetaRNN	Benign	0.076	T
MetaSVM	Benign	-0.35	T
MutationAssessor	Benign	1.3	L
PhyloP100		0.25
PrimateAI	Benign	0.23	T
PROVEAN	Benign	-0.15	N
REVEL	Benign	0.13
Sift	Benign	0.51	T
Sift4G	Benign	0.49	T
Polyphen		0.0080	B
Vest4		0.061
MutPred		0.21		Gain of catalytic residue at E109 (P = 0.1745)
MVP		0.75
MPC		0.59
ClinPred		0.032	T
GERP RS		1.5
PromoterAI		-0.0094	Neutral
Varity_R		0.22
gMVP		0.82
Mutation Taster		=93/7	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17875899; hg19: chrX-70330483;