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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:Q9Y240AlphaFoldGenCCjaxSfariGnomADPubmed

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

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