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
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- 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:
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:
- 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