CRLF3

cytokine receptor like factor 3, the group of Fibronectin type III domain containing

Basic information

Region (hg38): 17:30769388-30824692

Links

ENSG00000176390 ∙ NCBI:51379 ∙ OMIM:614853 ∙ HGNC:17177 ∙ Uniprot:Q8IUI8 ∙ 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 CRLF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CRLF3 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			16			16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	0	0

Variants in CRLF3

This is a list of pathogenic ClinVar variants found in the CRLF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-30784246-C-G		not specified	Uncertain significance (Mar 07, 2023)
17-30784255-G-C		not specified	Uncertain significance (Oct 07, 2024)
17-30785948-C-T		not specified	Uncertain significance (Jan 23, 2023)
17-30785961-C-T		not specified	Uncertain significance (Mar 22, 2023)
17-30785979-C-G		not specified	Uncertain significance (May 01, 2024)
17-30786030-C-T		not specified	Uncertain significance (May 30, 2024)
17-30792460-A-C		not specified	Uncertain significance (Mar 23, 2022)
17-30792477-C-A		not specified	Uncertain significance (Apr 12, 2022)
17-30792497-G-A		not specified	Uncertain significance (Nov 17, 2023)
17-30793467-G-C		not specified	Uncertain significance (Dec 15, 2023)
17-30793556-G-T		not specified	Uncertain significance (Oct 07, 2024)
17-30793570-C-T		not specified	Uncertain significance (Aug 09, 2021)
17-30793594-C-T		not specified	Uncertain significance (Aug 19, 2023)
17-30793600-C-G		not specified	Uncertain significance (Mar 06, 2023)
17-30793651-G-C		not specified	Uncertain significance (Feb 16, 2023)
17-30796300-A-T		not specified	Uncertain significance (Sep 25, 2024)
17-30803931-C-T		not specified	Uncertain significance (Oct 29, 2024)
17-30804009-G-A		not specified	Uncertain significance (Jan 04, 2022)
17-30824540-G-A		not specified	Uncertain significance (Feb 28, 2023)
17-30824618-G-C		not specified	Uncertain significance (May 17, 2023)
17-30824628-C-A		not specified	Uncertain significance (Sep 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CRLF3	protein_coding	protein_coding	ENST00000324238	8	55389

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000480	0.998	125684	0	64	125748	0.000255

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	195	244	0.798	0.0000125	2870
Missense in Polyphen		59	87.224	0.67642		1064
Synonymous	-0.977	104	92.1	1.13	0.00000487	868
Loss of Function	2.81	10	25.2	0.397	0.00000156	256

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000206	0.000206
Ashkenazi Jewish	0.00	0.00
East Asian	0.000870	0.000870
Finnish	0.000952	0.000693
European (Non-Finnish)	0.000202	0.000185
Middle Eastern	0.000870	0.000870
South Asian	0.000131	0.000131
Other	0.000344	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the negative regulation of cell cycle progression. {ECO:0000269|PubMed:19427400}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.612
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.25

Haploinsufficiency Scores

• pHI: 0.429
• hipred: Y
• hipred_score: 0.608
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.521

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Crlf3
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: G1/S transition of mitotic cell cycle;negative regulation of cell growth;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of JAK-STAT cascade;positive regulation of cell cycle arrest
• Cellular component: nucleus;cytoplasm;cytosol;plasma membrane
• Molecular function: DNA binding;protein binding;identical protein binding