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GeneBe

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

ENSG00000105472NCBI:6320OMIM:604713HGNC:10576Uniprot:Q9Y240AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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 (14 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.

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
14
clinvar
14
nonsense
0
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 14 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 Inborn genetic diseases Uncertain significance (Jul 27, 2022)2303815
19-50723586-G-A Inborn genetic diseases Uncertain significance (Nov 18, 2022)2239720
19-50723647-G-A Inborn genetic diseases Uncertain significance (Oct 26, 2022)2359954
19-50723951-A-C Inborn genetic diseases Uncertain significance (Aug 19, 2023)2592348
19-50724029-C-A Inborn genetic diseases Uncertain significance (Feb 03, 2022)2275703
19-50724046-G-C Inborn genetic diseases Uncertain significance (Dec 06, 2022)2298550
19-50724569-G-T Inborn genetic diseases Uncertain significance (May 26, 2023)2522113
19-50724581-G-A Inborn genetic diseases Uncertain significance (Jul 06, 2021)2234581
19-50724595-T-G Inborn genetic diseases Uncertain significance (May 04, 2022)2287106
19-50725078-G-A Inborn genetic diseases Uncertain significance (Dec 05, 2022)2332936
19-50725130-C-T Inborn genetic diseases Uncertain significance (Aug 10, 2021)2374722
19-50725283-C-T Inborn genetic diseases Uncertain significance (Dec 28, 2022)2340208
19-50725312-G-C Inborn genetic diseases Uncertain significance (Jan 10, 2023)2455844
19-50725314-C-CGCCCA Likely benign (Mar 29, 2018)785833
19-50725433-G-A Inborn genetic diseases Uncertain significance (Mar 29, 2022)2280478

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CLEC11Aprotein_codingprotein_codingENST00000250340 42389
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0003800.85312507646581257380.00264
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.4071881731.090.000008052012
Missense in Polyphen6060.3110.99484697
Synonymous0.4477277.00.9350.00000371669
Loss of Function1.29711.80.5945.17e-7130

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.01580.0153
Ashkenazi Jewish0.007230.00687
East Asian0.0003300.000326
Finnish0.000.00
European (Non-Finnish)0.002460.00224
Middle Eastern0.0003300.000326
South Asian0.0001320.000131
Other0.004460.00392

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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