CRLF2

cytokine receptor like factor 2, the group of Fibronectin type III domain containing|Pseudoautosomal region 1

Basic information

Region (hg38): Y:1190490-1212723

Links

∙ NCBI:64109 ∙ OMIM:300357, 400023 ∙ HGNC:14281 ∙ Uniprot:Q9HC73 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CRLF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRLF2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

Variants in CRLF2

This is a list of pathogenic ClinVar variants found in the CRLF2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Phenotype	Significance	ClinVar
Y-1196817-C-T	not specified	not provided (Sep 19, 2013)	133950
Y-1196852-A-C	Lymphoblastic leukemia, acute, with lymphomatous features	Pathogenic (Oct 02, 2014)	376003
Y-1198571-C-T	not specified	not provided (Sep 19, 2013)	133949
Y-1202479-C-T	not specified	not provided (Sep 19, 2013)	133948
Y-1206513-T-C	not specified	not provided (Sep 19, 2013)	133946
Y-1206592-C-T	not specified	not provided (Sep 19, 2013)	133947

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRLF2	protein_coding	protein_coding	ENST00000381567	6	16727

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.31e-7	0.342	124338	0	150	124488	0.000603

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.853	178	149	1.20	0.00000809	1658
Missense in Polyphen		51	40.385	1.2628		495
Synonymous	-1.07	75	64.1	1.17	0.00000418	489
Loss of Function	0.520	11	13.0	0.845	5.64e-7	136

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000429	0.000428
Ashkenazi Jewish	0.00109	0.00109
East Asian	0.000446	0.000445
Finnish	0.000604	0.000603
European (Non-Finnish)	0.000901	0.000896
Middle Eastern	0.000446	0.000445
South Asian	0.0000981	0.0000980
Other	0.000497	0.000496

dbNSFP

Source: dbNSFP

Function: FUNCTION: Receptor for thymic stromal lymphopoietin (TSLP). Forms a functional complex with TSLP and IL7R which is capable of stimulating cell proliferation through activation of STAT3 and STAT5. Also activates JAK2 (By similarity). Implicated in the development of the hematopoietic system. {ECO:0000250, ECO:0000269|PubMed:11418668}.;
Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;Thymic Stromal LymphoPoietin (TSLP) Signaling Pathway (Consensus)

Haploinsufficiency Scores

pHI
hipred: N
hipred_score: 0.353
ghis: 0.403

Essentials

essential_gene_CRISPR
essential_gene_CRISPR2
essential_gene_gene_trap
gene_indispensability_pred: E
gene_indispensability_score: 0.754

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Crlf2
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; respiratory system phenotype; immune system phenotype; digestive/alimentary phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype;

Gene ontology

Biological process: positive regulation of cell population proliferation;cytokine-mediated signaling pathway;positive regulation of mast cell activation;interleukin-7-mediated signaling pathway;positive regulation of STAT cascade;positive regulation of interleukin-5 secretion
Cellular component: extracellular region;plasma membrane;external side of plasma membrane;integral component of membrane;receptor complex
Molecular function: cytokine receptor activity;cytokine binding