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

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLEC11A gene.

• Inborn genetic diseases (11 variants)
• not provided (1 variants)

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			11			11
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice variant						0
non coding						0
Total	0	0	11	1	0

Variants in CLEC11A

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

Position	Type	Phenotype	Significance	ClinVar
19-50723556-G-A		Inborn genetic diseases	Uncertain significance (Jul 27, 2022)
19-50723586-G-A		Inborn genetic diseases	Uncertain significance (Nov 18, 2022)
19-50723647-G-A		Inborn genetic diseases	Uncertain significance (Oct 26, 2022)
19-50723951-A-C		Inborn genetic diseases	Uncertain significance (Aug 19, 2023)
19-50724029-C-A		Inborn genetic diseases	Uncertain significance (Feb 03, 2022)
19-50724046-G-C		Inborn genetic diseases	Uncertain significance (Dec 06, 2022)
19-50724569-G-T		Inborn genetic diseases	Uncertain significance (May 26, 2023)
19-50724581-G-A		Inborn genetic diseases	Uncertain significance (Jul 06, 2021)
19-50724595-T-G		Inborn genetic diseases	Uncertain significance (May 04, 2022)
19-50725078-G-A		Inborn genetic diseases	Uncertain significance (Dec 05, 2022)
19-50725130-C-T		Inborn genetic diseases	Uncertain significance (Aug 10, 2021)
19-50725283-C-T		Inborn genetic diseases	Uncertain significance (Dec 28, 2022)
19-50725312-G-C		Inborn genetic diseases	Uncertain significance (Jan 10, 2023)
19-50725314-C-CGCCCA			Likely benign (Mar 29, 2018)
19-50725433-G-A		Inborn genetic diseases	Uncertain significance (Mar 29, 2022)

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