CLEC11A

C-type lectin domain containing 11A, the group of C-type lectin domain containing

Basic information

Region (hg38): 19:50723363-50725708

Previous symbols: [ "SCGF" ]

Links

ENSG00000105472 ∙ NCBI:6320 ∙ OMIM:604713 ∙ HGNC:10576 ∙ Uniprot:Q9Y240 ∙ 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 CLEC11A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC11A 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			18			18
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in CLEC11A

This is a list of pathogenic ClinVar variants found in the CLEC11A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-50723556-G-A		not specified	Uncertain significance (Jul 27, 2022)
19-50723586-G-A		not specified	Uncertain significance (Nov 18, 2022)
19-50723647-G-A		not specified	Uncertain significance (Oct 26, 2022)
19-50723951-A-C		not specified	Uncertain significance (Aug 19, 2023)
19-50724029-C-A		not specified	Uncertain significance (Feb 03, 2022)
19-50724046-G-C		not specified	Uncertain significance (Dec 06, 2022)
19-50724432-C-G		not specified	Uncertain significance (Jan 18, 2022)
19-50724569-G-T		not specified	Uncertain significance (May 26, 2023)
19-50724581-G-A		not specified	Uncertain significance (Jul 06, 2021)
19-50724595-T-G		not specified	Uncertain significance (May 04, 2022)
19-50725078-G-A		not specified	Uncertain significance (Dec 05, 2022)
19-50725124-G-A		not specified	Uncertain significance (Dec 08, 2023)
19-50725124-G-T		not specified	Uncertain significance (Jan 08, 2024)
19-50725130-C-T		not specified	Uncertain significance (Aug 10, 2021)
19-50725283-C-T		not specified	Uncertain significance (Dec 28, 2022)
19-50725312-G-C		not specified	Uncertain significance (Jan 10, 2023)
19-50725314-C-CGCCCA			Likely benign (Mar 29, 2018)
19-50725433-G-A		not specified	Uncertain significance (Mar 29, 2022)
19-50725456-T-C		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC11A	protein_coding	protein_coding	ENST00000250340	4	2389

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000380	0.853	125076	4	658	125738	0.00264

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.407	188	173	1.09	0.00000805	2012
Missense in Polyphen		60	60.311	0.99484		697
Synonymous	0.447	72	77.0	0.935	0.00000371	669
Loss of Function	1.29	7	11.8	0.594	5.17e-7	130

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0158	0.0153
Ashkenazi Jewish	0.00723	0.00687
East Asian	0.000330	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.00246	0.00224
Middle Eastern	0.000330	0.000326
South Asian	0.000132	0.000131
Other	0.00446	0.00392

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Promotes osteogenesis by stimulating the differentiation of mesenchymal progenitors into mature osteoblasts (PubMed:27976999). Important for repair and maintenance of adult bone (By similarity). {ECO:0000250|UniProtKB:O88200, ECO:0000269|PubMed:27976999}.

Recessive Scores

• pRec: 0.173

Haploinsufficiency Scores

• pHI: 0.252
• hipred: N
• hipred_score: 0.297
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clec11a
• Phenotype: limbs/digits/tail phenotype; skeleton phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); hematopoietic system phenotype; homeostasis/metabolism phenotype; cellular phenotype

Gene ontology

• Biological process: ossification;positive regulation of cell population proliferation;regulation of signaling receptor activity
• Cellular component: extracellular region;extracellular space;cytoplasm
• Molecular function: growth factor activity;carbohydrate binding