CKLF

chemokine like factor

Basic information

Region (hg38): 16:66552563-66566251

Previous symbols: [ "CKLF1" ]

Links

ENSG00000217555 ∙ NCBI:51192 ∙ OMIM:616074 ∙ HGNC:13253 ∙ Uniprot:Q9UBR5 ∙ 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 CKLF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CKLF 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					1	1
missense			4	1		5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	1	1

Variants in CKLF

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

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

Position	Type	Phenotype	Significance	ClinVar
16-66552728-C-A		not specified	Likely benign (Dec 21, 2023)
16-66558277-A-G		not specified	Uncertain significance (May 02, 2024)
16-66563170-G-A		not specified	Uncertain significance (Jul 08, 2021)
16-66563192-C-A		not specified	Uncertain significance (Jun 24, 2022)
16-66565890-T-C		not specified	Uncertain significance (Jul 05, 2022)
16-66565923-A-G		not specified	Uncertain significance (Mar 25, 2024)
16-66565924-C-G		not specified	Uncertain significance (Nov 17, 2023)
16-66565987-G-A			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CKLF	protein_coding	protein_coding	ENST00000264001	4	13689

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00495	0.711	125727	0	10	125737	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.121	91	87.8	1.04	0.00000464	978
Missense in Polyphen		32	28.688	1.1155		333
Synonymous	1.18	25	33.7	0.741	0.00000196	308
Loss of Function	0.727	4	5.91	0.677	3.16e-7	66

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000945	0.0000944
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000536	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000711	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an important role in inflammation and regeneration of skeletal muscle. Partly inhibited by interleukin 10. {ECO:0000269|PubMed:11415443}.

Recessive Scores

• pRec: 0.0955

Intolerance Scores

• loftool: 0.413
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.148
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0225

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cklf

Gene ontology

• Biological process: cell population proliferation;regulation of signaling receptor activity;neutrophil chemotaxis;secretion by cell;macrophage chemotaxis;lymphocyte chemotaxis
• Cellular component: extracellular region;extracellular space;membrane;integral component of membrane
• Molecular function: chemokine activity