rs138899368

Variant names:

• chrX-1202479-C-A
• rs138899368
• NM_022148.4:c.406G>T

Your query was ambiguous. Multiple possible variants found:

• chrX-1202479-C-A
• chrX-1202479-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 3P and 2B. PM2 PP2 BP4_Moderate

The NM_022148.4(CRLF2):​c.406G>T​(p.Val136Leu) 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. 14/18 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. V136M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 31)
• Consequence: CRLF2 NM_022148.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 0 publications found

Genes affected

CRLF2 (HGNC:14281): (cytokine receptor like factor 2) This gene encodes a member of the type I cytokine receptor family. The encoded protein is a receptor for thymic stromal lymphopoietin (TSLP). Together with the interleukin 7 receptor (IL7R), the encoded protein and TSLP activate STAT3, STAT5, and JAK2 pathways, which control processes such as cell proliferation and development of the hematopoietic system. Rearrangement of this gene with immunoglobulin heavy chain gene (IGH) on chromosome 14, or with P2Y purinoceptor 8 gene (P2RY8) on the same X or Y chromosomes is associated with B-progenitor acute lymphoblastic leukemia (ALL) and Down syndrome ALL. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2014]

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 1 curated pathogenic missense variants (we use a threshold of 10). The gene has 0 curated benign missense variants. Gene score misZ: -0.85264 (below the threshold of 3.09). Trascript score misZ: NaN (below the threshold of 3.09).
• BP4: Computational evidence support a benign effect (MetaRNN=0.20258373).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022148.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRLF2	NM_022148.4	MANE Select	c.406G>T	p.Val136Leu	missense	Exon 4 of 8	NP_071431.2
	CRLF2	NM_001012288.3		c.70G>T	p.Val24Leu	missense	Exon 3 of 7	NP_001012288.2	Q9HC73-3
	CRLF2	NR_110830.2		n.418G>T		non_coding_transcript_exon	Exon 4 of 8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CRLF2	ENST00000400841.8	TSL:1 MANE Select	c.406G>T	p.Val136Leu	missense	Exon 4 of 8	ENSP00000383641.3	Q9HC73-1
	CRLF2	ENST00000381567.8	TSL:1	c.70G>T	p.Val24Leu	missense	Exon 3 of 7	ENSP00000370979.4	Q9HC73-3
	CRLF2	ENST00000467626.6	TSL:5	n.403G>T		non_coding_transcript_exon	Exon 4 of 8	ENSP00000485269.1	A0A0C4DH06

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	14
DANN	Benign	0.86
DEOGEN2	Benign	0.064	T
FATHMM_MKL	Benign	0.0030	N
LIST_S2	Benign	0.49	T
M_CAP	Benign	0.026	D
MetaRNN	Benign	0.20	T
MetaSVM	Benign	-0.92	T
MutationAssessor	Benign	2.0	M
PhyloP100		0.069
PrimateAI	Uncertain	0.70	T
PROVEAN	Benign	-0.66	N
REVEL	Benign	0.19
Sift	Benign	0.052	T
Sift4G	Uncertain	0.044	D
Polyphen		0.97	D
Vest4		0.27
MutPred		0.66		Gain of phosphorylation at T137 (P = 0.2378)
MVP		0.53
MPC		0.30
ClinPred		0.47	T
GERP RS		0.32
Varity_R		0.19
Mutation Taster		=92/8	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: rs138899368; hg19: chrX-1321349;