CLEC2L

C-type lectin domain family 2 member L, the group of C-type lectin domain containing

Basic information

Region (hg38): 7:139523685-139544985

Links

ENSG00000236279 ∙ NCBI:154790 ∙ ∙ HGNC:21969 ∙ Uniprot:P0C7M8 ∙ 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 CLEC2L gene.

• not_specified (39 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC2L gene is commonly pathogenic or not. These statistics are base on transcript: NM_001080511.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			39			39
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	39	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC2L	protein_coding	protein_coding	ENST00000422142	5	21129

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0143	0.881	124024	0	9	124033	0.0000363

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.527	83	97.7	0.850	0.00000631	1355
Missense in Polyphen		28	28.956	0.96697		314
Synonymous	0.703	37	42.9	0.863	0.00000324	452
Loss of Function	1.35	4	8.18	0.489	4.35e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000598	0.0000598
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000148	0.000141
European (Non-Finnish)	0.0000187	0.0000178
Middle Eastern	0.00	0.00
South Asian	0.0000690	0.0000658
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.680
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.208
• ghis: 0.623

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.344

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clec2l

Gene ontology

• Cellular component: integral component of membrane
• Molecular function: carbohydrate binding