CLNK

cytokine dependent hematopoietic cell linker, the group of SH2 domain containing

Basic information

Region (hg38): 4:10486394-10684768

Links

ENSG00000109684 ∙ NCBI:116449 ∙ OMIM:611434 ∙ HGNC:17438 ∙ Uniprot:Q7Z7G1 ∙ 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 CLNK gene.

• Inborn genetic diseases (18 variants)
• not specified (2 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLNK 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				2	1	3
missense			14	4	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	6	2

Variants in CLNK

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

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

Position	Type	Phenotype	Significance	ClinVar
4-10490475-G-A		not specified	Uncertain significance (Nov 28, 2023)
4-10490490-T-G		not specified	Uncertain significance (Aug 13, 2021)
4-10490492-A-T		not specified	Uncertain significance (Jul 12, 2022)
4-10490534-C-T		not specified	Uncertain significance (Jan 30, 2024)
4-10490563-A-G			Likely benign (Feb 01, 2023)
4-10490589-T-A		not specified	Uncertain significance (Dec 20, 2023)
4-10501258-C-T		not specified	Uncertain significance (Aug 30, 2022)
4-10501259-A-T		not specified	Uncertain significance (Jun 05, 2023)
4-10501299-C-T		not specified	Uncertain significance (Jan 04, 2022)
4-10501311-C-T		not specified	Uncertain significance (Mar 01, 2024)
4-10501312-G-A		CLNK-related disorder	Likely benign (Feb 10, 2022)
4-10501313-T-G		not specified	Benign (Mar 29, 2016)
4-10501342-A-G		not specified	Likely benign (Jul 13, 2021)
4-10513477-C-G		not specified	Uncertain significance (Feb 28, 2023)
4-10513558-C-A		not specified	Uncertain significance (Dec 08, 2023)
4-10513576-G-T		not specified	Uncertain significance (Oct 10, 2023)
4-10520793-C-G		not specified	Uncertain significance (Feb 21, 2024)
4-10520820-G-A		not specified	Likely benign (Dec 27, 2023)
4-10525844-C-A		not specified	Uncertain significance (May 31, 2023)
4-10525848-T-C		CLNK-related disorder	Likely benign (Feb 28, 2023)
4-10525850-G-T		not specified	Uncertain significance (Jun 21, 2022)
4-10540545-C-T		not specified	Uncertain significance (Dec 20, 2023)
4-10540556-C-T			Likely benign (Jul 01, 2023)
4-10540572-G-T		not specified	Uncertain significance (Oct 27, 2022)
4-10540602-G-C		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLNK	protein_coding	protein_coding	ENST00000226951	18	198471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.73e-29	0.00000146	124540	0	104	124644	0.000417

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.560	243	220	1.11	0.0000113	2810
Missense in Polyphen		65	57.902	1.1226		698
Synonymous	-0.964	88	77.2	1.14	0.00000425	730
Loss of Function	-1.76	38	27.9	1.36	0.00000126	364

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00136	0.00135
Ashkenazi Jewish	0.0000995	0.0000994
East Asian	0.00109	0.00106
Finnish	0.0000471	0.0000464
European (Non-Finnish)	0.000369	0.000363
Middle Eastern	0.00109	0.00106
South Asian	0.000510	0.000490
Other	0.000331	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the regulation of immunoreceptor signaling, including PLC-gamma-mediated B-cell antigen receptor (BCR) signaling and FC-epsilon R1-mediated mast cell degranulation. Involved in phosphorylation of LAT (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.558
• rvis_EVS: 0.69
• rvis_percentile_EVS: 85.21

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.267

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clnk
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: immune response;transmembrane receptor protein tyrosine kinase signaling pathway;positive regulation of signal transduction;intracellular signal transduction
• Molecular function: SH3/SH2 adaptor activity;protein binding